1
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Sokolova A, Johnstone KJ, McCart Reed AE, Simpson PT, Lakhani SR. Hereditary breast cancer: syndromes, tumour pathology and molecular testing. Histopathology 2023; 82:70-82. [PMID: 36468211 PMCID: PMC10953374 DOI: 10.1111/his.14808] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/12/2022] [Accepted: 09/18/2022] [Indexed: 12/09/2022]
Abstract
Hereditary factors account for a significant proportion of breast cancer risk. Approximately 20% of hereditary breast cancers are attributable to pathogenic variants in the highly penetrant BRCA1 and BRCA2 genes. A proportion of the genetic risk is also explained by pathogenic variants in other breast cancer susceptibility genes, including ATM, CHEK2, PALB2, RAD51C, RAD51D and BARD1, as well as genes associated with breast cancer predisposition syndromes - TP53 (Li-Fraumeni syndrome), PTEN (Cowden syndrome), CDH1 (hereditary diffuse gastric cancer), STK11 (Peutz-Jeghers syndrome) and NF1 (neurofibromatosis type 1). Polygenic risk, the cumulative risk from carrying multiple low-penetrance breast cancer susceptibility alleles, is also a well-recognised contributor to risk. This review provides an overview of the established breast cancer susceptibility genes as well as breast cancer predisposition syndromes, highlights distinct genotype-phenotype correlations associated with germline mutation status and discusses molecular testing and therapeutic implications in the context of hereditary breast cancer.
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Affiliation(s)
- A Sokolova
- Sullivan and Nicolaides PathologyBrisbane
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - K J Johnstone
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
| | - A E McCart Reed
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - P T Simpson
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
| | - S R Lakhani
- Centre for Clinical Research, Faculty of MedicineThe University of QueenslandBrisbane
- Pathology Queensland, The Royal Brisbane and Women's HospitalBrisbaneQueenslandAustralia
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2
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Ren M, Zhang S, Ma S, Zhang Q. Gene-environment interaction identification via penalized robust divergence. Biom J 2022; 64:461-480. [PMID: 34725857 PMCID: PMC9386692 DOI: 10.1002/bimj.202000157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 06/01/2021] [Accepted: 08/23/2021] [Indexed: 12/11/2022]
Abstract
In high-throughput cancer studies, gene-environment interactions associated with outcomes have important implications. Some commonly adopted identification methods do not respect the "main effect, interaction" hierarchical structure. In addition, they can be challenged by data contamination and/or long-tailed distributions, which are not uncommon. In this article, robust methods based on γ$\gamma$ -divergence and density power divergence are proposed to accommodate contaminated data/long-tailed distributions. A hierarchical sparse group penalty is adopted for regularized estimation and selection and can identify important gene-environment interactions and respect the "main effect, interaction" hierarchical structure. The proposed methods are implemented using an effective group coordinate descent algorithm. Simulation shows that when contamination occurs, the proposed methods can significantly outperform the existing alternatives with more accurate identification. The proposed approach is applied to the analysis of The Cancer Genome Atlas (TCGA) triple-negative breast cancer data and Gene Environment Association Studies (GENEVA) Type 2 Diabetes data.
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Affiliation(s)
- Mingyang Ren
- School of Mathematics Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China,Key Laboratory of Big Data Mining and Knowledge Management, Chinese Academy of Sciences, Beijing, P. R. China
| | - Sanguo Zhang
- School of Mathematics Sciences, University of Chinese Academy of Sciences, Beijing, P. R. China,Key Laboratory of Big Data Mining and Knowledge Management, Chinese Academy of Sciences, Beijing, P. R. China
| | - Shuangge Ma
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Qingzhao Zhang
- Department of Statistics and Data Science, School of Economics, Wang Yanan Institute for Studies in Economics, Fujian Key Lab of Statistics, Xiamen University, Fujian, P. R. China
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3
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Wiggins GAR, Black MA, Dunbier A, Morley-Bunker AE, Pearson JF, Walker LC. Increased gene expression variability in BRCA1-associated and basal-like breast tumours. Breast Cancer Res Treat 2021; 189:363-375. [PMID: 34287743 PMCID: PMC8357684 DOI: 10.1007/s10549-021-06328-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 07/07/2021] [Indexed: 11/21/2022]
Abstract
Purpose Inherited variants in the cancer susceptibility genes, BRCA1 and BRCA2 account for up to 5% of breast cancers. Multiple gene expression studies have analysed gene expression patterns that maybe associated with BRCA12 pathogenic variant status; however, results from these studies lack consensus. These studies have focused on the differences in population means to identified genes associated with BRCA1/2-carriers with little consideration for gene expression variability, which is also under genetic control and is a feature of cellular function. Methods We measured differential gene expression variability in three of the largest familial breast cancer datasets and a 2116 breast cancer meta-cohort. Additionally, we used RNA in situ hybridisation to confirm expression variability of EN1 in an independent cohort of more than 500 breast tumours. Results BRCA1-associated breast tumours exhibited a 22.8% (95% CI 22.3–23.2) increase in transcriptome-wide gene expression variability compared to BRCAx tumours. Additionally, 40 genes were associated with BRCA1-related breast cancers that had ChIP-seq data suggestive of enriched EZH2 binding. Of these, two genes (EN1 and IGF2BP3) were significantly variable in both BRCA1-associated and basal-like breast tumours. RNA in situ analysis of EN1 supported a significant (p = 6.3 × 10−04) increase in expression variability in BRCA1-associated breast tumours. Conclusion Our novel results describe a state of increased gene expression variability in BRCA1-related and basal-like breast tumours. Furthermore, genes with increased variability may be driven by changes in DNA occupancy of epigenetic effectors. The variation in gene expression is replicable and led to the identification of novel associations between genes and disease phenotypes. Supplementary Information The online version contains supplementary material available at 10.1007/s10549-021-06328-y.
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Affiliation(s)
- George A R Wiggins
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Anita Dunbier
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Arthur E Morley-Bunker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | | | - John F Pearson
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.,Biostatistics and Computational Biology Unit, University of Otago, Christchurch, New Zealand
| | - Logan C Walker
- Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
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4
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Zhou J, Zhou XA, Zhang N, Wang J. Evolving insights: how DNA repair pathways impact cancer evolution. Cancer Biol Med 2020; 17:805-827. [PMID: 33299637 PMCID: PMC7721097 DOI: 10.20892/j.issn.2095-3941.2020.0177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/10/2020] [Indexed: 12/17/2022] Open
Abstract
Viewing cancer as a large, evolving population of heterogeneous cells is a common perspective. Because genomic instability is one of the fundamental features of cancer, this intrinsic tendency of genomic variation leads to striking intratumor heterogeneity and functions during the process of cancer formation, development, metastasis, and relapse. With the increased mutation rate and abundant diversity of the gene pool, this heterogeneity leads to cancer evolution, which is the major obstacle in the clinical treatment of cancer. Cells rely on the integrity of DNA repair machineries to maintain genomic stability, but these machineries often do not function properly in cancer cells. The deficiency of DNA repair could contribute to the generation of cancer genomic instability, and ultimately promote cancer evolution. With the rapid advance of new technologies, such as single-cell sequencing in recent years, we have the opportunity to better understand the specific processes and mechanisms of cancer evolution, and its relationship with DNA repair. Here, we review recent findings on how DNA repair affects cancer evolution, and discuss how these mechanisms provide the basis for critical clinical challenges and therapeutic applications.
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Affiliation(s)
- Jiadong Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Xiao Albert Zhou
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
| | - Ning Zhang
- Laboratory of Cancer Cell Biology, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China.,Biomedical Pioneering Innovation Center (BIOPIC) and Translational Cancer Research Center, School of Life Sciences, First Hospital, Peking University, Beijing 100871, China
| | - Jiadong Wang
- Department of Radiation Medicine, Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China
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5
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Genome-Wide Gene Expression Analyses of BRCA1- and BRCA2-Associated Breast and Ovarian Tumours. Cancers (Basel) 2020; 12:cancers12103015. [PMID: 33081408 PMCID: PMC7603076 DOI: 10.3390/cancers12103015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 09/28/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
Germline pathogenic variants in BRCA1 and BRCA2 increase cumulative lifetime risk up to 75% for breast cancer and 76% for ovarian cancer. Genetic testing for BRCA1 and BRCA2 pathogenic variants has become an important part of clinical practice for cancer risk assessment and for reducing individual risk of developing cancer. Genetic testing can produce three outcomes: positive (a pathogenic variant), uninformative (no pathogenic variant) and uncertain significance (a variant of unknown clinical significance). More than one third of BRCA1 and BRCA2 variants identified have been classified as variants of uncertain significance, presenting a challenge for clinicians. To address this important clinical challenge, a number of studies have been undertaken to establish a gene expression phenotype for pathogenic BRCA1 and BRCA2 variant carriers in several diseased and normal tissues. However, the consistency of gene expression phenotypes described in studies has been poor. To determine if gene expression analysis has been a successful approach for variant classification, we describe the design and comparability of 23 published gene expression studies that have profiled cells from BRCA1 and BRCA2 pathogenic variant carriers. We show the impact of advancements in expression-based technologies, the importance of developing larger study cohorts and the necessity to better understand variables affecting gene expression profiles across different tissue types.
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6
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Privat M, Cavard A, Zekri Y, Ponelle-Chachuat F, Molnar I, Sonnier N, Bignon YJ. A high expression ratio of RhoA/RhoB is associated with the migratory and invasive properties of basal-like Breast Tumors. Int J Med Sci 2020; 17:2799-2808. [PMID: 33162807 PMCID: PMC7645338 DOI: 10.7150/ijms.43101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 09/14/2020] [Indexed: 01/11/2023] Open
Abstract
Basal-like breast cancer is among the most aggressive cancers and there is still no effective targeted treatment. In order to identify new therapeutic targets, we performed mRNA-Seq on eight breast cancer cell lines. Among the genes overexpressed in basal-like tumors, we focused on the RhoA and RhoB genes, which encode small GTPases known to play a role in the actin cytoskeleton, allowing cells to migrate. qRT-PCR and Western blotting were used for expression studies. Migratory and invasive properties were analysed by wound healing and Boyden chambers assays. Stress fibers formation was evaluated by fluorescent actin labeling. Rho siRNA, small inhibitor Rhosin treatment and BRCA1 transfection were performed to study the role of Rho and BRCA1 proteins. We showed that strong expression of RhoA and low expression of RhoB was associated with the basal-like subtype of breast cancer. Decreasing RhoA expression reduced the migratory and invasive capacities of basal-like cell lines, while decreasing RhoB expression increased these capacities. Rhosin, an inhibitor of RhoA, could also reduce the migration of basal-like cell lines. Rho proteins are involved in the formation of stress fibers, a conformation of the actin cytoskeleton found in migrating cells: inhibition of RhoA expression decreased the formation of these fibers. BRCA1, a gene frequently inactivated in basal-like tumors, appears to play a role in the differential expression of RhoA and RhoB in these tumors, as the restoration of BRCA1 expression in a BRCA1-mutated basal-like cell line decreased expression of RhoA and increased expression of RhoB, resulting in reduced migratory capacity. These results suggest Rho proteins as potential therapeutic targets for basal-like and BRCA1-mutated breast cancer, as migration and acquisition of mesenchymal properties are key functional pathways in these tumors with high metastatic potential.
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Affiliation(s)
- Maud Privat
- INSERM U1240 IMoST, University of Clermont Auvergne, Clermont-Ferrand, F-63000, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
| | - Amélie Cavard
- Département d'Oncogénétique, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
| | - Yanis Zekri
- Département d'Oncogénétique, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
| | - Flora Ponelle-Chachuat
- INSERM U1240 IMoST, University of Clermont Auvergne, Clermont-Ferrand, F-63000, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
| | - Ioana Molnar
- INSERM U1240 IMoST, University of Clermont Auvergne, Clermont-Ferrand, F-63000, France
- Centre d'Investigation Clinique UMR 501, F-63001 Clermont-Ferrand, France
- Department of clinical research, Délégation Recherche Clinique et Innovation, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
| | - Nicolas Sonnier
- INSERM U1240 IMoST, University of Clermont Auvergne, Clermont-Ferrand, F-63000, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
- Centre de Ressources Biologiques BB-0033-00075, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
| | - Yves-Jean Bignon
- INSERM U1240 IMoST, University of Clermont Auvergne, Clermont-Ferrand, F-63000, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
- Centre de Ressources Biologiques BB-0033-00075, Centre Jean Perrin, F-63011 Clermont-Ferrand, France
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7
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Incorvaia L, Fanale D, Badalamenti G, Bono M, Calò V, Cancelliere D, Castiglia M, Fiorino A, Pivetti A, Barraco N, Cutaia S, Russo A, Bazan V. Hereditary Breast and Ovarian Cancer in Families from Southern Italy (Sicily)-Prevalence and Geographic Distribution of Pathogenic Variants in BRCA1/2 Genes. Cancers (Basel) 2020; 12:E1158. [PMID: 32380732 PMCID: PMC7280980 DOI: 10.3390/cancers12051158] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 05/01/2020] [Accepted: 05/03/2020] [Indexed: 12/20/2022] Open
Abstract
Recent advances in the detection of germline pathogenic variants (PVs) in BRCA1/2 genes have allowed a deeper understanding of the BRCA-related cancer risk. Several studies showed a significant heterogeneity in the prevalence of PVs across different populations. Because little is known about this in the Sicilian population, our study was aimed at investigating the prevalence and geographic distribution of inherited BRCA1/2 PVs in families from this specific geographical area of Southern Italy. We retrospectively collected and analyzed all clinical information of 1346 hereditary breast and/or ovarian cancer patients genetically tested for germline BRCA1/2 PVs at University Hospital Policlinico "P. Giaccone" of Palermo from January 1999 to October 2019. Thirty PVs were more frequently observed in the Sicilian population but only some of these showed a specific territorial prevalence, unlike other Italian and European regions. This difference could be attributed to the genetic heterogeneity of the Sicilian people and its historical background. Therefore hereditary breast and ovarian cancers could be predominantly due to BRCA1/2 PVs different from those usually detected in other geographical areas of Italy and Europe. Our investigation led us to hypothesize that a higher prevalence of some germline BRCA PVs in Sicily could be a population-specific genetic feature of BRCA-positive carriers.
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Affiliation(s)
- Lorena Incorvaia
- Department of Biomedicine, Neuroscience and Advanced Diagnostics (Bi.N.D.), Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy;
| | - Daniele Fanale
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Giuseppe Badalamenti
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Marco Bono
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Valentina Calò
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Daniela Cancelliere
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Marta Castiglia
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Alessia Fiorino
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Alessia Pivetti
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Nadia Barraco
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Sofia Cutaia
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Antonio Russo
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
| | - Viviana Bazan
- Department of Surgical, Oncological and Oral Sciences, Section of Medical Oncology, University of Palermo, 90127 Palermo, Italy; (D.F.); (G.B.); (M.B.); (V.C.); (D.C.); (M.C.); (A.F.); (A.P.); (N.B.); (S.C.); (V.B.)
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8
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Li Z, Zhang X, Hou C, Zhou Y, Chen J, Cai H, Ye Y, Liu J, Huang N. Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer. Int J Oncol 2019; 56:522-530. [PMID: 31894314 PMCID: PMC6959384 DOI: 10.3892/ijo.2019.4950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/30/2019] [Indexed: 12/27/2022] Open
Abstract
Triple‑negative breast cancer (TNBC) accounts for ~15% of all breast cancer diagnoses each year. Patients with TNBC tend to have a higher risk for early relapse and a worse prognosis. TNBC is characterized by extensive somatic copy number alterations (CNAs). However, the DNA CNA profile of TNBC remains to be extensively investigated. The present study assessed the genomic profile of CNAs in 201 TNBC samples, aiming to identify recurrent CNAs that may drive the pathogenesis of TNBC. In total, 123 regions of significant amplification and deletion were detected using the Genomic Identification of Significant Targets in Cancer algorithm, and potential driver genes for TNBC were identified. A total of 31 samples exhibited signs of chromothripsis and revealed chromosome pulverization hotspot regions. The present study further determined 199 genomic locations that were significantly enriched for breakpoints, which indicated TNBC‑specific genomic instability regions. Unsupervised hierarchical clustering of tumors resulted in three main subgroups that exhibited distinct CNA profiles, which may reveal the heterogeneity of molecular mechanisms in TNBC subgroups. These results will extend the molecular understanding of TNBC and will facilitate the discovery of therapeutic and diagnostic target candidates.
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Affiliation(s)
- Zaibing Li
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Xiao Zhang
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Chenxin Hou
- West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Yuqing Zhou
- West China Medical School, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Junli Chen
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
| | - Haoyang Cai
- Center of Growth, Metabolism and Aging, Key Laboratory of Bio‑Resources and Eco‑Environment, College of Life Sciences, Sichuan University, Chengdu, Sichuan 610064, P.R. China
| | - Yifeng Ye
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Jinping Liu
- Department of Breast Surgery, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, Sichuan 611731, P.R. China
| | - Ning Huang
- Department of Pathophysiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, Sichuan 610041, P.R. China
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9
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Geenen JJJ, Linn SC, Beijnen JH, Schellens JHM. PARP Inhibitors in the Treatment of Triple-Negative Breast Cancer. Clin Pharmacokinet 2019; 57:427-437. [PMID: 29063517 DOI: 10.1007/s40262-017-0587-4] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Breast cancer is a heterogeneous disease, manifesting in a broad differentiation in phenotypes and morphologic profiles, resulting in variable clinical behavior. Between 10 and 20% of all breast cancers are triple negative. Triple-negative breast cancer (TNBC) lacks the expression of human epidermal growth factor receptor 2 (HER2) and hormone receptors; therefore, to date, chemotherapy remains the backbone of treatment. TNBC tends to be aggressive and has a high histological grade, resulting in a poor 5-year prognosis. It has a high prevalence of BRCA1 mutations and an increased Ki-67 expression. This subtype usually responds well to taxanes and/or platinum compounds and poly (ADP-ribose) polymerase (PARP) inhibitors. Studies with PARP inhibitors have demonstrated promising results in the treatment of BRCA-mutated breast and ovarian cancer, and PARP inhibitors have been studied as monotherapy and in combination with cytotoxic therapy or radiotherapy. PARP inhibitor efficacy on poly (ADP-ribose) polymer (PAR) formation in vivo can be quantified by pharmacodynamic assays that measure PAR activity in peripheral blood mononuclear cells (PBMC). Biomarkers such as TP53, ATM, PALB2 and RAD51C might be prognostic or predictive indicators for treatment response, and could also provide targets for novel treatment strategies. In summary, this review provides an overview of the treatment options for basal-like TNBC, including PARP inhibitors, and focuses on the pharmacotherapeutic options in these patients.
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Affiliation(s)
- Jill J J Geenen
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Sabine C Linn
- Department of Molecular Pathology, Antoni van Leeuwenhoek Hospital, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands.,Department of Pathology, Utrecht University Medical Center, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands
| | - Jos H Beijnen
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Department of Pharmacy, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.,Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands
| | - Jan H M Schellens
- Department of Clinical Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands. .,Division of Pharmacology, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands. .,Division of Medical Oncology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands. .,Department of Pharmacy, The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands. .,Utrecht Institute for Pharmaceutical Sciences (UIPS), Utrecht University, Utrecht, The Netherlands.
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10
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Nones K, Johnson J, Newell F, Patch AM, Thorne H, Kazakoff SH, de Luca XM, Parsons MT, Ferguson K, Reid LE, McCart Reed AE, Srihari S, Lakis V, Davidson AL, Mukhopadhyay P, Holmes O, Xu Q, Wood S, Leonard C, Beesley J, Harris JM, Barnes D, Degasperi A, Ragan MA, Spurdle AB, Khanna KK, Lakhani SR, Pearson JV, Nik-Zainal S, Chenevix-Trench G, Waddell N, Simpson PT. Whole-genome sequencing reveals clinically relevant insights into the aetiology of familial breast cancers. Ann Oncol 2019; 30:1071-1079. [PMID: 31090900 PMCID: PMC6637375 DOI: 10.1093/annonc/mdz132] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Whole-genome sequencing (WGS) is a powerful method for revealing the diversity and complexity of the somatic mutation burden of tumours. Here, we investigated the utility of tumour and matched germline WGS for understanding aetiology and treatment opportunities for high-risk individuals with familial breast cancer. PATIENTS AND METHODS We carried out WGS on 78 paired germline and tumour DNA samples from individuals carrying pathogenic variants in BRCA1 (n = 26) or BRCA2 (n = 22) or from non-carriers (non-BRCA1/2; n = 30). RESULTS Matched germline/tumour WGS and somatic mutational signature analysis revealed patients with unreported, dual pathogenic germline variants in cancer risk genes (BRCA1/BRCA2; BRCA1/MUTYH). The strategy identified that 100% of tumours from BRCA1 carriers and 91% of tumours from BRCA2 carriers exhibited biallelic inactivation of the respective gene, together with somatic mutational signatures suggestive of a functional deficiency in homologous recombination. A set of non-BRCA1/2 tumours also had somatic signatures indicative of BRCA-deficiency, including tumours with BRCA1 promoter methylation, and tumours from carriers of a PALB2 pathogenic germline variant and a BRCA2 variant of uncertain significance. A subset of 13 non-BRCA1/2 tumours from early onset cases were BRCA-proficient, yet displayed complex clustered structural rearrangements associated with the amplification of oncogenes and pathogenic germline variants in TP53, ATM and CHEK2. CONCLUSIONS Our study highlights the role that WGS of matched germline/tumour DNA and the somatic mutational signatures can play in the discovery of pathogenic germline variants and for providing supporting evidence for variant pathogenicity. WGS-derived signatures were more robust than germline status and other genomic predictors of homologous recombination deficiency, thus impacting the selection of platinum-based or PARP inhibitor therapy. In this first examination of non-BRCA1/2 tumours by WGS, we illustrate the considerable heterogeneity of these tumour genomes and highlight that complex genomic rearrangements may drive tumourigenesis in a subset of cases.
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Affiliation(s)
- K Nones
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Johnson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - F Newell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A M Patch
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - H Thorne
- kConFab Investigators, The Peter MacCallum Cancer Centre, Melbourne, VIC; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, VIC
| | - S H Kazakoff
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - X M de Luca
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - M T Parsons
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K Ferguson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - L E Reid
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - A E McCart Reed
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD
| | - S Srihari
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - V Lakis
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - A L Davidson
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD; Faculty of Medicine, The University of Queensland, Brisbane, QLD
| | - P Mukhopadhyay
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - O Holmes
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - Q Xu
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Wood
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - C Leonard
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J Beesley
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - J M Harris
- Faculty of Health, School Biomedical Science - Queensland University of Technology, Brisbane, QLD, Australia
| | - D Barnes
- Department of Public Health and Primary Care, Centre for Cancer Genetic Epidemiology, University of Cambridge, Cambridge
| | - A Degasperi
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - M A Ragan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD
| | - A B Spurdle
- Molecular Cancer Epidemiology Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - K K Khanna
- Signal Transduction Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S R Lakhani
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD; Royal Brisbane & Women's Hospital, Pathology Queensland, Brisbane, QLD, Australia
| | - J V Pearson
- Genome Informatics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - S Nik-Zainal
- MRC Cancer Unit, Hutchison/MRC Research Centre, University of Cambridge, Cambridge; Department of Medical Genetics, The Clinical School, University of Cambridge, Cambridge, UK
| | - G Chenevix-Trench
- Cancer Genetics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD
| | - N Waddell
- Medical Genomics Group, QIMR Berghofer Medical Research Institute, Brisbane, QLD.
| | - P T Simpson
- Faculty of Medicine, Centre for Clinical Research, The University of Queensland, Brisbane, QLD.
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11
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Yadav S, Couch FJ. Germline Genetic Testing for Breast Cancer Risk: The Past, Present, and Future. Am Soc Clin Oncol Educ Book 2019; 39:61-74. [PMID: 31099663 DOI: 10.1200/edbk_238987] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The field of germline genetic testing for breast cancer (BC) risk has evolved substantially in the last decade. The introduction of multigene panel testing (MGPT) led to an urgent need to understand the cancer risk associated with several genes included in the panels. Although the research on understanding the cancer risk associated with mutations in several genes continues, there is also a need to understand the modifying effects of race and ethnicity, family history, and BC pathology on the prevalence of germline mutations and associated BC risk. Furthermore, polygenic risk scores (PRSs) to predict BC risk in patients with or without germline mutations in cancer-predisposition genes are now available for clinical use, although data on the clinical utility of PRSs are lacking. In patients with advanced BC associated with BRCA1/2 mutation, olaparib and talazoparib are now approved for treatment. In addition, molecular profiling studies are being used to clarify the BC tumor biology in mutation carriers to identify potential therapeutic options. In this article, we discuss these advances in the field of germline genetic testing and highlight current limitations and implications for clinical care.
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Affiliation(s)
| | - Fergus J Couch
- 2 Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
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12
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Sønderstrup IMH, Jensen MB, Ejlertsen B, Eriksen JO, Gerdes AM, Kruse TA, Larsen MJ, Thomassen M, Laenkholm AV. Evaluation of tumor-infiltrating lymphocytes and association with prognosis in BRCA-mutated breast cancer. Acta Oncol 2019; 58:363-370. [PMID: 30614364 DOI: 10.1080/0284186x.2018.1539239] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Patients with a BRCA1 or BRCA2 mutation (BRCA-mutated breast cancer) are frequently diagnosed with low differentiated and highly proliferating breast cancer characterized by high amounts of tumor-infiltrating lymphocytes (Tils). Stromal Tils (sTils) are highly prognostic in sporadic triple-negative and HER2 positive breast cancer however, their prognostic importance in BRCA-mutated breast cancers is unknown. MATERIAL AND METHODS Formalin-fixed paraffin-embedded primary tumor tissue from 411 patients with a germline BRCA1 or BRCA2 mutation and diagnosed with early breast cancer was included. The percentage of sTils was quantified on full HE sections according to guidelines proposed by the Immuno-Oncology Biomarker in Breast Cancer Working Group. Distribution of sTils and associates with patient and tumor characteristics were assessed according to categorical sTils groups defined as low (<10%), intermediate (10-59%) and high (≥60%). Prognostic associations of sTils were evaluated as a continuous variable in univariate and multivariate models. Only follow-up time beyond date of BRCA mutation test was included. RESULTS A large proportion had high sTils (27% in the full cohort, 36% in BRCA1-mutated, and 44% in ER negative breast cancers). Higher sTils were associated with BRCA1, ER negative breast cancer, high histological grade and medullary histology. In combined analysis for BRCA1 and BRCA2-mutated breast cancers, increasing sTils in 10% intervals were significantly associated with OS (HR 0.92, 95% CI 0.84-1.00, p = .05). For each 10% increment of sTils in BRCA1 breast cancers, a 10% reduction of mortality (adjusted HR 0.90 95% CI 0.81-0.99, p = .03) and a 13% reduction in risk of DFS-event (HR 0.87 95% CI 0.76-1.00, p = .05) was observed even after adjustment for ER status. No significant association with survival was of observed in the BRCA2 subgroup. Test for interaction of sTils and BRCA status was not statistically significant (p = .3). CONCLUSIONS Breast cancer patients with a germline BRCA mutation had higher sTils than previously reported in sporadic breast cancers, and sTils were associated with favorable survival among BRCA carriers.
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Affiliation(s)
- I. M. H. Sønderstrup
- Department of Surgical Pathology Region Zealand, Zealand University Hospital, Slagelse, Denmark
| | - M. B. Jensen
- Danish Breast Cancer Cooperative Group, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - B. Ejlertsen
- Danish Breast Cancer Cooperative Group, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Department of Oncology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - J. O. Eriksen
- Department of Surgical Pathology Region Zealand, Zealand University Hospital, Slagelse, Denmark
| | - A. M. Gerdes
- Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - T. A. Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - M. J. Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - M. Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - A. V. Laenkholm
- Department of Surgical Pathology Region Zealand, Zealand University Hospital, Slagelse, Denmark
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13
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Sønderstrup IMH, Jensen MBR, Ejlertsen B, Eriksen JO, Gerdes AM, Kruse TA, Larsen MJ, Thomassen M, Lænkholm AV. Subtypes in BRCA-mutated breast cancer. Hum Pathol 2019; 84:192-201. [DOI: 10.1016/j.humpath.2018.10.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 09/29/2018] [Accepted: 10/04/2018] [Indexed: 01/06/2023]
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14
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Sonnenblick A, Venet D, Brohée S, Pondé N, Sotiriou C. pAKT pathway activation is associated with PIK3CA mutations and good prognosis in luminal breast cancer in contrast to p-mTOR pathway activation. NPJ Breast Cancer 2019; 5:7. [PMID: 30729154 PMCID: PMC6355773 DOI: 10.1038/s41523-019-0102-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2018] [Accepted: 01/08/2019] [Indexed: 12/19/2022] Open
Abstract
Numerous studies have focused on the PI3K/AKT/mTOR pathway in estrogen receptor positive (ER) breast cancer (BC), as a linear signal transduction pathway and reported its association with worse clinical outcomes. We developed gene signatures that reflect the level of expression of phosphorylated-Serine473-AKT (pAKT) and phosphorylated-Serine2448-mTOR (p-mTOR) separately, capturing their corresponding level of pathway activation. Our analysis revealed that the pAKT pathway activation was associated with luminal A BC while the p-mTOR pathway activation was more associated with luminal B BC (Kruskal-Wallis test p < 10-10). pAKT pathway activation was significantly associated with better outcomes (multivariable HR, 0.79; 95%CI, 0.74-0.85; p = 2.5 × 10-10) and PIK3CA mutations (p = 0.0001) whereas p-mTOR pathway activation showed worse outcomes (multivariable HR,1.1; 95%CI, 1.1-1.2; p = 9.9 × 10-4) and associated with p53 mutations (p = 0.04). in conclusion, our data show that pAKT and p-mTOR pathway activation have differing impact on prognosis and suggest that they are not linearly connected in luminal breast cancers.
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Affiliation(s)
- Amir Sonnenblick
- 1Oncology Division, Tel Aviv Sourasky Medical Center, and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Venet
- 2Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Sylvain Brohée
- 2Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Noam Pondé
- 2Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
| | - Christos Sotiriou
- 2Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium
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15
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Lee JS, Oh S, Park SK, Lee MH, Lee JW, Kim SW, Son BH, Noh DY, Lee JE, Park HL, Kim MJ, Cho SI, Lee YK, Park SS, Seong MW. Reclassification of BRCA1 and BRCA2 variants of uncertain significance: a multifactorial analysis of multicentre prospective cohort. J Med Genet 2018; 55:794-802. [PMID: 30415210 DOI: 10.1136/jmedgenet-2018-105565] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 08/27/2018] [Accepted: 08/29/2018] [Indexed: 11/03/2022]
Abstract
BACKGROUND BRCA1 and BRCA2 (BRCA1/2) variants classified ambiguously as variants of uncertain significance (VUS) are a major challenge for clinical genetic testing in breast cancer; their relevance to the cancer risk is unclear and the association with the response to specific BRCA1/2-targeted agents is uncertain. To minimise the proportion of VUS in BRCA1/2, we performed the multifactorial likelihood analysis and validated this method using an independent cohort of patients with breast cancer. METHODS We used a data set of 2115 patients with breast cancer from the nationwide multicentre prospective Korean Hereditary Breast Cancer study. In total, 83 BRCA1/2 VUSs (BRCA1, n=26; BRCA2, n=57) were analysed. The multifactorial probability was estimated by combining the prior probability with the overall likelihood ratio derived from co-occurrence of each VUS with pathogenic variants, personal and family history, and tumour characteristics. The classification was compared with the interpretation according to the American College of Medical Genetics and Genomics-Association for Molecular Pathology (ACMG/AMP) guidelines. An external validation was conducted using independent data set of 810 patients. RESULTS We were able to redefine 38 VUSs (BRCA1, n=10; BRCA2, n=28). The revised classification was highly correlated with the ACMG/AMP guideline-based interpretation (BRCA1, p for trend=0.015; BRCA2, p=0.001). Our approach reduced the proportion of VUS from 19% (154/810) to 8.9% (72/810) in the retrospective validation data set. CONCLUSION The classification in this study would minimise the 'uncertainty' in clinical interpretation, and this validated multifactorial model can be used for the reliable annotation of BRCA1/2 VUSs.
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Affiliation(s)
- Jee-Soo Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea.,Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sohee Oh
- Department of Biostatistics SMG-SNU Boramae Medical Center, Seoul, Republic of Korea
| | - Sue Kyung Park
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Min-Hyuk Lee
- Department of Surgery, College of Medicine, Soonchunhyang University, Seoul, Republic of Korea
| | - Jong Won Lee
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seongnam, Republic of Korea
| | - Sung-Won Kim
- Department of Surgery, Seoul National University Bundang Hospital, Seoul, Republic of Korea
| | - Byung Ho Son
- Department of Surgery, Asan Medical Center, University of Ulsan College of Medicine, Seongnam, Republic of Korea
| | - Dong-Young Noh
- Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jeong Eon Lee
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hai-Lin Park
- Department of Surgery, Kangnam CHA Hospital, Seoul, Republic of Korea
| | - Man Jin Kim
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Sung Im Cho
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Young Kyung Lee
- Department of Laboratory Medicine, Hallym University Sacred Heart Hospital, Anyang, Republic of Korea.,Department of Laboratory Medicine, Hallym University College of Medicine, Anyang, Republic of Korea
| | - Sung Sup Park
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Moon-Woo Seong
- Department of Laboratory Medicine, Seoul National University Hospital, Seoul National University College of Medicine, Seoul, Republic of Korea.,Cancer Research Institute, Seoul National University College of Medicine, Seoul, Republic of Korea
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16
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Akbari V, Kallhor M, Akbari MT. Transcriptome mining of non-BRCA1/A2 and BRCA1/A2 familial breast cancer. J Cell Biochem 2018; 120:575-583. [PMID: 30125992 DOI: 10.1002/jcb.27413] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/12/2018] [Indexed: 12/23/2022]
Abstract
About 10% of all breast cancer cases are the familial type. Mutations in two highly penetrance breast cancer susceptibility genes, BRCA1 and BRCA2, can only explain 20% to 25% of genetic susceptibility to breast cancer, and most familial breast cancer cases have intact BRCA1 and BRCA2 genes that refer to non-BRCA1/A2 or BRCAX familial breast cancer. Despite extensive studies, more than 50% of genetic susceptibility to breast cancer remained to be disclosed. Finding the differences between these two types of breast cancer (non-BRCA1/A2 and BRCA1/A2) at genomic, transcriptomic, and proteomic levels can help us to elucidate fundamental molecular processes and develope more promising therapeutic targets. Here, we used expression data of 391 patients with familial breast cancer including 195 non-BRCA1/A2 and 196 BRCA1 and/or BRCA2 cases from four independent studies by means of meta-analysis to find differences in gene expression signature between these two types of familial breast cancer. As well as, we applied comprehensive network analysis to find crucial protein complexes and regulators for each condition. Our results revealed significant overexpression of cell cycle processes in BRCA1/A2 patients and significant overexpression of estrogen axis in non-BRCA1/A2 patients. Moreover, we found FOXM1 as the central regulator of cell cycle processes and GATA3, FOXA1, and ESR1 as the main regulators of estrogen axis.
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Affiliation(s)
- Vahid Akbari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Marzieh Kallhor
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammad Taghi Akbari
- Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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17
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Chen CC, Feng W, Lim PX, Kass EM, Jasin M. Homology-Directed Repair and the Role of BRCA1, BRCA2, and Related Proteins in Genome Integrity and Cancer. ANNUAL REVIEW OF CANCER BIOLOGY 2018; 2:313-336. [PMID: 30345412 PMCID: PMC6193498 DOI: 10.1146/annurev-cancerbio-030617-050502] [Citation(s) in RCA: 193] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Germ-line and somatic mutations in genes that promote homology-directed repair (HDR), especially BRCA1 and BRCA2, are frequently observed in several cancers, in particular, breast and ovary but also prostate and other cancers. HDR is critical for the error-free repair of DNA double-strand breaks and other lesions, and HDR factors also protect stalled replication forks. As a result, loss of BRCA1 or BRCA2 poses significant risks to genome integrity, leading not only to cancer predisposition but also to sensitivity to DNA-damaging agents, affecting therapeutic approaches. Here we review recent advances in our understanding of BRCA1 and BRCA2, including how they genetically interact with other repair factors, how they protect stalled replication forks, how they affect the response to aldehydes, and how loss of their functions links to mutation signatures. Importantly, given the recent advances with poly(ADP-ribose) polymerase inhibitors (PARPi) for the treatment of HDR-deficient tumors, we discuss mechanisms by which BRCA-deficient tumors acquire resistance to PARPi and other agents.
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Affiliation(s)
- Chun-Chin Chen
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Pei Xin Lim
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Elizabeth M Kass
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065
- Graduate School of Medical Sciences, Weill Cornell Medicine, New York, NY 10065
- Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, NY 10065
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18
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Privat M, Rudewicz J, Sonnier N, Tamisier C, Ponelle-Chachuat F, Bignon YJ. Antioxydation And Cell Migration Genes Are Identified as Potential Therapeutic Targets in Basal-Like and BRCA1 Mutated Breast Cancer Cell Lines. Int J Med Sci 2018; 15:46-58. [PMID: 29333087 PMCID: PMC5765739 DOI: 10.7150/ijms.20508] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 10/11/2017] [Indexed: 12/26/2022] Open
Abstract
Basal-like breast cancers are among the most aggressive cancers and effective targeted therapies are still missing. In order to identify new therapeutic targets, we performed Methyl-Seq and RNA-Seq of 10 breast cancer cell lines with different phenotypes. We confirmed that breast cancer subtypes cluster the RNA-Seq data but not the Methyl-Seq data. Basal-like tumor hypermethylated phenotype was not confirmed in our study but RNA-Seq analysis allowed to identify 77 genes significantly overexpressed in basal-like breast cancer cell lines. Among them, 48 were overexpressed in triple negative breast cancers of TCGA data. Some molecular functions were overrepresented in this candidate gene list. Genes involved in antioxydation, such as SOD1, MGST3 and PRDX or cadherin-binding genes, such as PFN1, ITGB1 and ANXA1, could thus be considered as basal like breast cancer biomarkers. We then sought if these genes were linked to BRCA1, since this gene is often inactivated in basal-like breast cancers. Nine genes were identified overexpressed in both basal-like breast cancer cells and BRCA1 mutated cells. Amongst them, at least 3 genes code for proteins implicated in epithelial cell migration and epithelial to mesenchymal transition (VIM, ITGB1 and RhoA). Our study provided several potential therapeutic targets for triple negative and BRCA1 mutated breast cancers. It seems that migration and mesenchymal properties acquisition of basal-like breast cancer cells is a key functional pathway in these tumors with a high metastatic potential.
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Affiliation(s)
- Maud Privat
- Université Clermont Auvergne, Centre Jean Perrin, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000 Clermont Ferrand, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63000 Clermont Ferrand, France
| | - Justine Rudewicz
- Département d'Oncogénétique, Centre Jean Perrin, F-63000 Clermont Ferrand, France
| | - Nicolas Sonnier
- Université Clermont Auvergne, Centre Jean Perrin, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000 Clermont Ferrand, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63000 Clermont Ferrand, France
- Biological Resources Center BB-0033-00075, Centre Jean Perrin, F-63000 Clermont Ferrand, France
| | - Christelle Tamisier
- Département d'Oncogénétique, Centre Jean Perrin, F-63000 Clermont Ferrand, France
| | - Flora Ponelle-Chachuat
- Université Clermont Auvergne, Centre Jean Perrin, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000 Clermont Ferrand, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63000 Clermont Ferrand, France
| | - Yves-Jean Bignon
- Université Clermont Auvergne, Centre Jean Perrin, INSERM, U1240 Imagerie Moléculaire et Stratégies Théranostiques, F-63000 Clermont Ferrand, France
- Département d'Oncogénétique, Centre Jean Perrin, F-63000 Clermont Ferrand, France
- Biological Resources Center BB-0033-00075, Centre Jean Perrin, F-63000 Clermont Ferrand, France
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Fresno C, González GA, Merino GA, Flesia AG, Podhajcer OL, Llera AS, Fernández EA. A novel non-parametric method for uncertainty evaluation of correlation-based molecular signatures: its application on PAM50 algorithm. Bioinformatics 2017; 33:693-700. [PMID: 28062443 DOI: 10.1093/bioinformatics/btw704] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 11/04/2016] [Indexed: 11/13/2022] Open
Abstract
Motivation The PAM50 classifier is used to assign patients to the highest correlated breast cancer subtype irrespectively of the obtained value. Nonetheless, all subtype correlations are required to build the risk of recurrence (ROR) score, currently used in therapeutic decisions. Present subtype uncertainty estimations are not accurate, seldom considered or require a population-based approach for this context. Results Here we present a novel single-subject non-parametric uncertainty estimation based on PAM50's gene label permutations. Simulations results ( n = 5228) showed that only 61% subjects can be reliably 'Assigned' to the PAM50 subtype, whereas 33% should be 'Not Assigned' (NA), leaving the rest to tight 'Ambiguous' correlations between subtypes. The NA subjects exclusion from the analysis improved survival subtype curves discrimination yielding a higher proportion of low and high ROR values. Conversely, all NA subjects showed similar survival behaviour regardless of the original PAM50 assignment. We propose to incorporate our PAM50 uncertainty estimation to support therapeutic decisions. Availability and Implementation Source code can be found in 'pbcmc' R package at Bioconductor. Contacts cristobalfresno@gmail.com or efernandez@bdmg.com.ar. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Cristóbal Fresno
- UA AREA CS. AGR. ING. BIO. Y S, CONICET, Universidad Católica de Córdoba, Córdoba 5016, Argentina
| | - Germán Alexis González
- UA AREA CS. AGR. ING. BIO. Y S, CONICET, Universidad Católica de Córdoba, Córdoba 5016, Argentina
| | | | - Ana Georgina Flesia
- CIEM-CONICET and FAMAF, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Osvaldo Luis Podhajcer
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir-CONICET, Buenos Aires 1405, Argentina
| | - Andrea Sabina Llera
- Laboratory of Molecular and Cellular Therapy, Instituto Leloir-CONICET, Buenos Aires 1405, Argentina
| | - Elmer Andrés Fernández
- UA AREA CS. AGR. ING. BIO. Y S, CONICET, Universidad Católica de Córdoba, Córdoba 5016, Argentina
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20
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Computational Investigation of Homologous Recombination DNA Repair Deficiency in Sporadic Breast Cancer. Sci Rep 2017; 7:15742. [PMID: 29146938 PMCID: PMC5691048 DOI: 10.1038/s41598-017-16138-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 11/03/2017] [Indexed: 12/17/2022] Open
Abstract
BRCAness has important implications in the management and treatment of patients with breast and ovarian cancer. In this study, we propose a computational framework to measure the BRCAness of breast and ovarian tumor samples based on their gene expression profiles. We define a characteristic profile for BRCAness by comparing gene expression differences between BRCA1/2 mutant familial tumors and sporadic breast cancer tumors while adjusting for relevant clinical factors. With this BRCAness profile, our framework calculates sample-specific BRCA scores, which indicates homologous recombination (HR)-mediated DNA repair pathway activity of samples. We found that in sporadic breast cancer high BRCAness score is associated with aberrant copy number of HR genes rather than somatic mutation and other genomic features. Moreover, we observed significant correlations of BRCA score with genome instability and neoadjuvant chemotherapy. More importantly, BRCA score provides significant prognostic value in both breast and ovarian cancers after considering established clinical variables. In summary, the inferred BRCAness from our framework can be used as a robust biomarker for the prediction of prognosis and treatment response in breast and ovarian cancers.
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21
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Abstract
Breast cancer 1 (BRCA1), as a tumor suppressor, exerts an effective influence on protecting DNA integrity to suppress the development of breast cancer (BC). BRCA1 expression is induced in response to DNA-damaging agents such as etoposide. Germline BRCA1 gene mutations are associated with development of hereditary BC. However, besides BRCA-mutated BCs, some sporadic cancers may also exhibit a BRCA-like phenotype, displaying so-called ‘BRCAness’. This common phenotype may respond to similar therapeutic approaches as BRCA-mutated tumors and may thus have important implications for the clinical management of these cancers. In order to determine whether and how etoposide regulates the protein levels of BRCA1 in BC cells, we exposed a panel of five selected cell lines to etoposide, compared the results to untreated control cells, and then stained the cells with the specific, reliable, and reproducible MS110 antibody directed against phosphorylated Ser1423 BRCA1. By evaluating cytoplasmic BRCA1 protein levels, we were able to distinguish three aggressive BC subtypes with BRCAness characteristics. In addition, determination of early and late apoptosis helped to complete the analysis of BRCA1 functions in the DNA damage pathway of aggressive BC. In conclusion, our study suggested that high cytoplasmic BRCA1 protein levels could be considered as a potential predictive marker for response to chemotherapy in both sporadic and hereditary BC. Tumors with either BRCAness phenotype or germline BRCA1 mutation are both aggressive BCs associated with poor prognosis and could both be subjected to targeted therapies against BRCA1-mutated BC in future clinical management strategies.
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22
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Shao F, Sun H, Deng CX. Potential therapeutic targets of triple-negative breast cancer based on its intrinsic subtype. Oncotarget 2017; 8:73329-73344. [PMID: 29069872 PMCID: PMC5641215 DOI: 10.18632/oncotarget.20274] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 08/06/2017] [Indexed: 12/13/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is an aggressive subgroup of human breast cancer, which is characterized as estrogen receptor (ER) negative, progesterone receptor (PR) negative, and human epidermal growth factor receptor 2 (HER2) negative. TNBC is the most difficult breast cancer subgroup to treat, due to its unresponsiveness to current clinical targeted therapies, high rate of recurrence, and poor prognosis. Thus, there is an urgent medical need to identify therapeutic targets and develop more effective stratified medicine for the treatment of TNBC. Here we review the potential therapeutic targets for TNBC based on its intrinsic subtype. We also review the aberrant activated signals found in different subgroups of TNBC, including androgen receptor (AR) and PI3K/AKT/mTOR, Notch, Wnt/β-catenin, Hedge-hog, and TGF-β signaling pathways, which play essential roles in multiple development stages of TNBC. The careful analysis of these signaling pathways and therapeutic targets would have significant impact on the drug development and clinical trials, leading to effective therapies for this deadly disease.
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Affiliation(s)
- Fangyuan Shao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Heng Sun
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Chu-Xia Deng
- Faculty of Health Sciences, University of Macau, Macau SAR, China
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23
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Transcriptional signature of lymphoblastoid cell lines of BRCA1, BRCA2 and non- BRCA1/2 high risk breast cancer families. Oncotarget 2017; 8:78691-78712. [PMID: 29108258 PMCID: PMC5667991 DOI: 10.18632/oncotarget.20219] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 07/17/2017] [Indexed: 12/20/2022] Open
Abstract
Approximately 25% of hereditary breast cancer cases are associated with a strong familial history which can be explained by mutations in BRCA1 or BRCA2 and other lower penetrance genes. The remaining high-risk families could be classified as BRCAX (non-BRCA1/2) families. Gene expression involving alternative splicing represents a well-known mechanism regulating the expression of multiple transcripts, which could be involved in cancer development. Thus using RNA-seq methodology, the analysis of transcriptome was undertaken to potentially reveal transcripts implicated in breast cancer susceptibility and development. RNA was extracted from immortalized lymphoblastoid cell lines of 117 women (affected and unaffected) coming from BRCA1, BRCA2 and BRCAX families. Anova analysis revealed a total of 95 transcripts corresponding to 85 different genes differentially expressed (Bonferroni corrected p-value <0.01) between those groups. Hierarchical clustering allowed distinctive subgrouping of BRCA1/2 subgroups from BRCAX individuals. We found 67 transcripts, which could discriminate BRCAX from BRCA1/BRCA2 individuals while 28 transcripts discriminate affected from unaffected BRCAX individuals. To our knowledge, this represents the first study identifying transcripts differentially expressed in lymphoblastoid cell lines from major classes of mutation-related breast cancer subgroups, namely BRCA1, BRCA2 and BRCAX. Moreover, some transcripts could discriminate affected from unaffected BRCAX individuals, which could represent potential therapeutic targets for breast cancer treatment.
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24
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Non-BRCA familial breast cancer: review of reported pathology and molecular findings. Pathology 2017; 49:363-370. [PMID: 28450088 DOI: 10.1016/j.pathol.2017.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/07/2017] [Accepted: 03/16/2017] [Indexed: 01/02/2023]
Abstract
The majority of women evaluated for a clinical concern of possible hereditary breast cancer syndromes have no identified pathogenic variants in genes predisposing them to breast cancer. Non-BRCA1- or BRCA2-related familial breast cancer, also called 'BRCAX', thus comprises a sizeable proportion of familial breast cancer but it is poorly understood. In this study, we reviewed 14 studies on histopathology and molecular studies of BRCAX to determine if there were differences between 'sporadic' breast cancers and compared to cancers arising in women harbouring variants in known cancer predisposition genes. Across available literature, there was inconsistency on inclusion and exclusion criteria, reported parameters, and use of controls. Cohorts were small, and while several studies reported findings that appeared to distinguish the BRCAX cases from sporadic and/or gene-positive controls, no findings were reported in more than one study. To determine whether the BRCAX families might still contain important genetic subsets awaiting discovery will require prospective ascertainment of a large number of women with familial breast cancer who are screened for all currently established predisposition genes, whose tumours are assessed for multiple parameters in a uniform manner, and in which controls (BRCA1/2+ and non-familial 'sporadic' cases) are collected from the same population.
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25
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Dhillon KK, Bajrami I, Taniguchi T, Lord CJ. Synthetic lethality: the road to novel therapies for breast cancer. Endocr Relat Cancer 2016; 23:T39-55. [PMID: 27528623 DOI: 10.1530/erc-16-0228] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Accepted: 08/15/2016] [Indexed: 12/12/2022]
Abstract
When the BRCA1 and BRCA2 tumour suppressor genes were identified in the early 1990s, the immediate implications of mapping, cloning and delineating the sequence of these genes were that individuals in families with a BRCA gene mutation could be tested for the presence of a mutation and their risk of developing cancer could be predicted. Over time though, the discovery of BRCA1 and BRCA2 has had a much greater influence than many might have imagined. In this review, we discuss how the discovery of BRCA1 and BRCA2 has not only provided an understanding of the molecular processes that drive tumourigenesis but also reignited an interest in therapeutically exploiting loss-of-function alterations in tumour suppressor genes.
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Affiliation(s)
| | - Ilirjana Bajrami
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
| | | | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
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26
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Park KS, Cho EY, Nam SJ, Ki CS, Kim JW. Comparative analysis of BRCA1 and BRCA2 variants of uncertain significance in patients with breast cancer: a multifactorial probability-based model versus ACMG standards and guidelines for interpreting sequence variants. Genet Med 2016; 18:1250-1257. [PMID: 27124784 DOI: 10.1038/gim.2016.39] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2015] [Accepted: 02/17/2016] [Indexed: 11/09/2022] Open
Abstract
PURPOSE To investigate variants of uncertain significance (VUS) in BRCA1 and BRCA2, we assessed the multifactorial posterior probability of VUS in BRCA1 and BRCA2 and compared these analyses with interpretations according to the recently released American College of Medical Genetics and Genomics (ACMG) standards and guidelines. METHODS The analysis involved 715 Korean patients with breast cancer. The multifactorial probability of a VUS was analyzed using the prior probability and combined likelihoods of personal and family history, the pathologic profile of the breast cancer, and co-occurrence with pathogenic variants. Results were compared with those obtained according to the ACMG standards/guidelines. RESULTS Sixteen VUS from 51 BRCA1 VUS carriers and 28 VUS from 62 BRCA2 VUS carriers were analyzed. There was a slight agreement between the two analyses, with a kappa value of 0.14 (95% confidence interval (CI) = -0.34 to 0.62) for the BRCA1 VUS and a kappa value of 0.17 (95% CI = -0.10 to 0.49) for the BRCA2 VUS. CONCLUSION We propose that genetic counseling should be based on the concordant results between these two analyses. When discrepancies are found, those variants are still considered VUS and careful counseling should be provided.Genet Med 18 12, 1250-1257.
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Affiliation(s)
| | - Eun Yoon Cho
- Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Seok Jin Nam
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Chang-Seok Ki
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jong-Won Kim
- Department of Laboratory Medicine and Genetics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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27
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Massink MPG, Kooi IE, Martens JWM, Waisfisz Q, Meijers-Heijboer H. Genomic profiling of CHEK2*1100delC-mutated breast carcinomas. BMC Cancer 2015; 15:877. [PMID: 26553136 PMCID: PMC4640207 DOI: 10.1186/s12885-015-1880-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 10/30/2015] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND CHEK2*1100delC is a moderate-risk breast cancer susceptibility allele with a high prevalence in the Netherlands. We performed copy number and gene expression profiling to investigate whether CHEK2*1100delC breast cancers harbor characteristic genomic aberrations, as seen for BRCA1 mutated breast cancers. METHODS We performed high-resolution SNP array and gene expression profiling of 120 familial breast carcinomas selected from a larger cohort of 155 familial breast tumors, including BRCA1, BRCA2, and CHEK2 mutant tumors. Gene expression analyses based on a mRNA immune signature was used to identify samples with relative low amounts of tumor infiltrating lymphocytes (TILs), which were previously found to disturb tumor copy number and LOH (loss of heterozygosity) profiling. We specifically compared the genomic and gene expression profiles of CHEK2*1100delC breast cancers (n = 14) with BRCAX (familial non-BRCA1/BRCA2/CHEK2*1100delC mutated) breast cancers (n = 34) of the luminal intrinsic subtypes for which both SNP-array and gene expression data is available. RESULTS High amounts of TILs were found in a relatively small number of luminal breast cancers as compared to breast cancers of the basal-like subtype. As expected, these samples mostly have very few copy number aberrations and no detectable regions of LOH. By unsupervised hierarchical clustering of copy number data we observed a great degree of heterogeneity amongst the CHEK2*1100delC breast cancers, comparable to the BRCAX breast cancers. Furthermore, copy number aberrations were mostly seen at low frequencies in both the CHEK2*1100delC and BRCAX group of breast cancers. However, supervised class comparison identified copy number loss of chromosomal arm 1p to be associated with CHEK2*1100delC status. CONCLUSIONS In conclusion, in contrast to basal-like BRCA1 mutated breast cancers, no apparent specific somatic copy number aberration (CNA) profile for CHEK2*1100delC breast cancers was found. With the possible exception of copy number loss of chromosomal arm 1p in a subset of tumors, which might be involved in CHEK2 tumorigenesis. This difference in CNAs profiles might be explained by the need for BRCA1-deficient tumor cells to acquire survival factors, by for example specific copy number aberrations, to expand. Such factors may not be needed for breast tumors with a defect in a non-essential gene such as CHEK2.
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Affiliation(s)
- Maarten P G Massink
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Irsan E Kooi
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - John W M Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Cancer Genomics Netherlands, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
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28
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Severson TM, Peeters J, Majewski I, Michaut M, Bosma A, Schouten PC, Chin SF, Pereira B, Goldgraben MA, Bismeijer T, Kluin RJC, Muris JJF, Jirström K, Kerkhoven RM, Wessels L, Caldas C, Bernards R, Simon IM, Linn S. BRCA1-like signature in triple negative breast cancer: Molecular and clinical characterization reveals subgroups with therapeutic potential. Mol Oncol 2015; 9:1528-38. [PMID: 26004083 PMCID: PMC5528786 DOI: 10.1016/j.molonc.2015.04.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 04/20/2015] [Accepted: 04/20/2015] [Indexed: 12/31/2022] Open
Abstract
Triple negative (TN) breast cancers make up some 15% of all breast cancers. Approximately 10-15% are mutant for the tumor suppressor, BRCA1. BRCA1 is required for homologous recombination-mediated DNA repair and deficiency results in genomic instability. BRCA1-mutated tumors have a specific pattern of genomic copy number aberrations that can be used to classify tumors as BRCA1-like or non-BRCA1-like. BRCA1 mutation, promoter methylation, BRCA1-like status and genome-wide expression data was determined for 112 TN breast cancer samples with long-term follow-up. Mutation status for 21 known DNA repair genes and PIK3CA was assessed. Gene expression and mutation frequency in BRCA1-like and non-BRCA1-like tumors were compared. Multivariate survival analysis was performed using the Cox proportional hazards model. BRCA1 germline mutation was identified in 10% of patients and 15% of tumors were BRCA1 promoter methylated. Fifty-five percent of tumors classified as BRCA1-like. The functions of genes significantly up-regulated in BRCA1-like tumors included cell cycle and DNA recombination and repair. TP53 was found to be frequently mutated in BRCA1-like (P < 0.05), while PIK3CA was frequently mutated in non-BRCA1-like tumors (P < 0.05). A significant association with worse prognosis was evident for patients with BRCA1-like tumors (adjusted HR = 3.32, 95% CI = 1.30-8.48, P = 0.01). TN tumors can be further divided into two major subgroups, BRCA1-like and non-BRCA1-like with different mutation and expression patterns and prognoses. Based on these molecular patterns, subgroups may be more sensitive to specific targeted agents such as PI3K or PARP inhibitors.
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Affiliation(s)
- Tesa M Severson
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Ian Majewski
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Magali Michaut
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Astrid Bosma
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Philip C Schouten
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | - Tycho Bismeijer
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Roelof J C Kluin
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jettie J F Muris
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Karin Jirström
- Department of Clinical Sciences, Division of Oncology and Pathology, Lund University, Lund, Sweden
| | - Ron M Kerkhoven
- Genomics Core Facility, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Lodewyk Wessels
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - René Bernards
- Division of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Sabine Linn
- Division of Molecular Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Division of Medical Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Pathology, University Medical Center Utrecht, The Netherlands.
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29
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Yan M, Shield-Artin K, Byrne D, Deb S, Waddell N, Haviv I, Fox SB. Comparative microRNA profiling of sporadic and BRCA1 associated basal-like breast cancers. BMC Cancer 2015; 15:506. [PMID: 26152113 PMCID: PMC4494690 DOI: 10.1186/s12885-015-1522-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 06/26/2015] [Indexed: 01/29/2023] Open
Abstract
Background While a number of studies have examined miRNA profiles across the molecular subtypes of breast cancer, it is unclear whether BRCA1 basal-like cancers have a specific miRNA profile. This study aims to compare grade independent miRNA expression in luminal cancers, sporadic and BRCA1 basal-type breast cancers. It also aims to ascertain an immunohistochemical profile regulated by BRCA1 specific miRNAs for potential diagnostic use. Methods miRNA expression was assessed in 11 BRCA1 basal, 16 sporadic basal, 17 luminal grade 3 cancers via microarrays. The expression of Cyclin D1, FOXP1, FIH-1, pan-ERβ, NRP1 and CD99, predicted to be regulated by BRCA1 specific miRNAs by computer prediction algorithms, was assessed via immunohistochemistry in a cohort of 35 BRCA1 and 52 sporadic basal-like cancers. Assessment of cyclin D1, FOXP1, NRP1 and CD99 expression was repeated on a validation cohort of 82 BRCA1 and 65 sporadic basal-like breast cancers. Results Unsupervised clustering of basal cancers resulted in a “sporadic” cluster of 11 cancers, and a “BRCA1” cluster of 16 cancers, including a subgroup composed entirely of 10 BRCA1 cancers. Compared with sporadic basal cancers, BRCA1 cancers showed reduced positivity for proteins predicted to be regulated by miRNAs: FOXP1 (6/20[30 %] vs. 37/49[76 %], p < 0.001), cyclin D1 (8/22[36 %] vs. 30/46[65 %], p = 0.025), NRP1 (2/20[10 %] vs. 23/46[50 %], p = 0.002). This was confirmed in the validation cohort (all p < 0.001). Negative staining for 2 or more out of FOXP1, cyclin D1 and NRP1 predicts germline BRCA1 mutation with a sensitivity of 92 %, specificity of 44 %, positive predictive value of 38 % and a negative predictive value of 94 %. Conclusion Sporadic and BRCA1 basal-like cancers have grade independent miRNA expression profiles. Furthermore miRNA driven differences in the expression of proteins in BRCA1 basal cancers may be detected via immunohistochemistry. These findings may have important diagnostic implications, as immunohistochemical assessment of basal cancers, in addition to the patient’s family and clinical history, may potentially identify patients who may benefit from BRCA1 gene testing. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1522-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Max Yan
- Department of Anatomical Pathology, Prince of Wales Hospital, School of Medical Sciences, University of New South Wales, Randwick, 2031, Australia.
| | | | - David Byrne
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, 3002, Australia.
| | - Siddhartha Deb
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, 3002, Australia.
| | - Nic Waddell
- Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, University of Queensland, St Lucia, Australia.
| | | | - Izhak Haviv
- Baker IDI Heart and Diabetes Institute, Prahran, 3004, Australia.
| | - Stephen B Fox
- Department of Pathology, Peter MacCallum Cancer Centre, East Melbourne, 3002, Australia.
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30
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Prakash R, Zhang Y, Feng W, Jasin M. Homologous recombination and human health: the roles of BRCA1, BRCA2, and associated proteins. Cold Spring Harb Perspect Biol 2015; 7:a016600. [PMID: 25833843 DOI: 10.1101/cshperspect.a016600] [Citation(s) in RCA: 561] [Impact Index Per Article: 62.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Homologous recombination (HR) is a major pathway for the repair of DNA double-strand breaks in mammalian cells, the defining step of which is homologous strand exchange directed by the RAD51 protein. The physiological importance of HR is underscored by the observation of genomic instability in HR-deficient cells and, importantly, the association of cancer predisposition and developmental defects with mutations in HR genes. The tumor suppressors BRCA1 and BRCA2, key players at different stages of HR, are frequently mutated in familial breast and ovarian cancers. Other HR proteins, including PALB2 and RAD51 paralogs, have also been identified as tumor suppressors. This review summarizes recent findings on BRCA1, BRCA2, and associated proteins involved in human disease with an emphasis on their molecular roles and interactions.
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Affiliation(s)
- Rohit Prakash
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Yu Zhang
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Weiran Feng
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
| | - Maria Jasin
- Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065 Louis V. Gerstner Jr. Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065
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31
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Massink MPG, Kooi IE, van Mil SE, Jordanova ES, Ameziane N, Dorsman JC, van Beek DM, van der Voorn JP, Sie D, Ylstra B, van Deurzen CHM, Martens JW, Smid M, Sieuwerts AM, de Weerd V, Foekens JA, van den Ouweland AMW, van Dyk E, Nederlof PM, Waisfisz Q, Meijers-Heijboer H. Proper genomic profiling of (BRCA1-mutated) basal-like breast carcinomas requires prior removal of tumor infiltrating lymphocytes. Mol Oncol 2015; 9:877-88. [PMID: 25616998 PMCID: PMC5528776 DOI: 10.1016/j.molonc.2014.12.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Revised: 12/20/2014] [Accepted: 12/27/2014] [Indexed: 01/02/2023] Open
Abstract
INTRODUCTION BRCA1-mutated breast carcinomas may have distinct biological features, suggesting the involvement of specific oncogenic pathways in tumor development. The identification of genomic aberrations characteristic for BRCA1-mutated breast carcinomas could lead to a better understanding of BRCA1-associated oncogenic events and could prove valuable in clinical testing for BRCA1-involvement in patients. METHODS For this purpose, genomic and gene expression profiles of basal-like BRCA1-mutated breast tumors (n = 27) were compared with basal-like familial BRCAX (non-BRCA1/2/CHEK2*1100delC) tumors (n = 14) in a familial cohort of 120 breast carcinomas. RESULTS Genome wide copy number profiles of the BRCA1-mutated breast carcinomas in our data appeared heterogeneous. Gene expression analyses identified varying amounts of tumor infiltrating lymphocytes (TILs) as a major cause for this heterogeneity. Indeed, selecting tumors with relative low amounts of TILs, resulted in the identification of three known but also five previously unrecognized BRCA1-associated copy number aberrations. Moreover, these aberrations occurred with high frequencies in the BRCA1-mutated tumor samples. Using these regions it was possible to discriminate BRCA1-mutated from BRCAX breast carcinomas, and they were validated in two independent cohorts. To further substantiate our findings, we used flow cytometry to isolate cancer cells from formalin-fixed, paraffin-embedded, BRCA1-mutated triple negative breast carcinomas with estimated TIL percentages of 40% and higher. Genomic profiles of sorted and unsorted fractions were compared by shallow whole genome sequencing and confirm our findings. CONCLUSION This study shows that genomic profiling of in particular basal-like, and thus BRCA1-mutated, breast carcinomas is severely affected by the presence of high numbers of TILs. Previous reports on genomic profiling of BRCA1-mutated breast carcinomas have largely neglected this. Therefore, our findings have direct consequences on the interpretation of published genomic data. Also, these findings could prove valuable in light of currently used genomic tools for assessing BRCA1-involvement in breast cancer patients and pathogenicity assessment of BRCA1 variants of unknown significance. The BRCA1-associated genomic aberrations identified in this study provide possible leads to a better understanding of BRCA1-associated oncogenesis.
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Affiliation(s)
- Maarten P G Massink
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Irsan E Kooi
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Saskia E van Mil
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Ekaterina S Jordanova
- Department of Obstetrics and Gynaecology, Center for Gynaecologic Oncology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Najim Ameziane
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Josephine C Dorsman
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Daphne M van Beek
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | | | - Daoud Sie
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Bauke Ylstra
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
| | - Carolien H M van Deurzen
- Department of Pathology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - John W Martens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Marcel Smid
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Anieta M Sieuwerts
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Vanja de Weerd
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - John A Foekens
- Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Ans M W van den Ouweland
- Department of Clinical Genetics, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands.
| | - Ewald van Dyk
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Petra M Nederlof
- Department of Molecular Carcinogenesis, Netherlands Cancer Institute, Amsterdam, The Netherlands.
| | - Quinten Waisfisz
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
| | - Hanne Meijers-Heijboer
- Department of Clinical Genetics, VU University Medical Center, Amsterdam, The Netherlands.
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32
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Srihari S, Madhamshettiwar PB, Song S, Liu C, Simpson PT, Khanna KK, Ragan MA. Complex-based analysis of dysregulated cellular processes in cancer. BMC SYSTEMS BIOLOGY 2014; 8 Suppl 4:S1. [PMID: 25521701 PMCID: PMC4290683 DOI: 10.1186/1752-0509-8-s4-s1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Background Differential expression analysis of (individual) genes is often used to study their roles in diseases. However, diseases such as cancer are a result of the combined effect of multiple genes. Gene products such as proteins seldom act in isolation, but instead constitute stable multi-protein complexes performing dedicated functions. Therefore, complexes aggregate the effect of individual genes (proteins) and can be used to gain a better understanding of cancer mechanisms. Here, we observe that complexes show considerable changes in their expression, in turn directed by the concerted action of transcription factors (TFs), across cancer conditions. We seek to gain novel insights into cancer mechanisms through a systematic analysis of complexes and their transcriptional regulation. Results We integrated large-scale protein-interaction (PPI) and gene-expression datasets to identify complexes that exhibit significant changes in their expression across different conditions in cancer. We devised a log-linear model to relate these changes to the differential regulation of complexes by TFs. The application of our model on two case studies involving pancreatic and familial breast tumour conditions revealed: (i) complexes in core cellular processes, especially those responsible for maintaining genome stability and cell proliferation (e.g. DNA damage repair and cell cycle) show considerable changes in expression; (ii) these changes include decrease and countering increase for different sets of complexes indicative of compensatory mechanisms coming into play in tumours; and (iii) TFs work in cooperative and counteractive ways to regulate these mechanisms. Such aberrant complexes and their regulating TFs play vital roles in the initiation and progression of cancer. Conclusions Complexes in core cellular processes display considerable decreases and countering increases in expression, strongly reflective of compensatory mechanisms in cancer. These changes are directed by the concerted action of cooperative and counteractive TFs. Our study highlights the roles of these complexes and TFs and presents several case studies of compensatory processes, thus providing novel insights into cancer mechanisms.
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Roessler J, Ammerpohl O, Gutwein J, Steinemann D, Schlegelberger B, Weyer V, Sariyar M, Geffers R, Arnold N, Schmutzler R, Bartram CR, Heinrich T, Abbas M, Antonopoulos W, Schipper E, Hasemeier B, Kreipe H, Lehmann U. The CpG island methylator phenotype in breast cancer is associated with the lobular subtype. Epigenomics 2014; 7:187-99. [PMID: 25347269 DOI: 10.2217/epi.14.74] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Aberrations in DNA methylation patterns are well-described in human malignancies. However, the existence of the 'CpG island methylator phenotype' (CIMP) in human breast cancer is still controversial. MATERIALS & METHODS Illumina's HumanMethylation 450K BeadChip was used to analyze genome-wide DNA methylation patterns. Chromosomal abnormalities were determined by array-based CGH. RESULTS Invasive lobular breast carcinomas exhibit the highest number of differentially methylated CpG sites and a strong inverse correlation of aberrant DNA hypermethylation and copy number alterations. Nine differentially methylated regions within seven genes discriminating the investigated subgroups were identified and validated in an independent validation cohort and correlated to a better relapse-free survival. CONCLUSION These results depict a clear difference between genetically and epigenetically unstable breast carcinomas indicating different ways of tumor progression and/or initiation, which strongly supports the association of CIMP with the lobular subtype and provide new options for detection and therapy.
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Affiliation(s)
- Jessica Roessler
- Institute of Pathology, Hannover Medical School, Carl-Neuber-Str. 1, D-30625 Hannover, Germany
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Larsen MJ, Thomassen M, Gerdes AM, Kruse TA. Hereditary breast cancer: clinical, pathological and molecular characteristics. BREAST CANCER-BASIC AND CLINICAL RESEARCH 2014; 8:145-55. [PMID: 25368521 PMCID: PMC4213954 DOI: 10.4137/bcbcr.s18715] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/02/2023]
Abstract
Pathogenic mutations in BRCA1 or BRCA2 are only detected in 25% of families with a strong history of breast cancer, though hereditary factors are expected to be involved in the remaining families with no recognized mutation. Molecular characterization is expected to provide new insight into the tumor biology to guide the search of new high-risk alleles and provide better classification of the growing number of BRCA1/2 variants of unknown significance (VUS). In this review, we provide an overview of hereditary breast cancer, its genetic background, and clinical implications, before focusing on the pathologically and molecular features associated with the disease. Recent transcriptome and genome profiling studies of tumor series from BRCA1/2 mutation carriers as well as familial non-BRCA1/2 will be discussed. Special attention is paid to its association with molecular breast cancer subtypes as well as the latest advances in predicting BRCA1/2 involvement (BRCAness) using molecular signatures, for improved diagnostics and selection of patients sensitive to targeted therapeutics.
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Affiliation(s)
- Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Torben A Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark. ; Human Genetics, Institute of Clinical Research, University of Southern Denmark, Odense, Denmark
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Taherian-Fard A, Srihari S, Ragan MA. Breast cancer classification: linking molecular mechanisms to disease prognosis. Brief Bioinform 2014; 16:461-74. [PMID: 24950687 DOI: 10.1093/bib/bbu020] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Accepted: 05/07/2014] [Indexed: 12/21/2022] Open
Abstract
Breast cancer was traditionally perceived as a single disease; however, recent advances in gene expression and genomic profiling have revealed that breast cancer is in fact a collection of diseases exhibiting distinct anatomical features, responses to treatment and survival outcomes. Consequently, a number of schemes have been proposed for subtyping of breast cancer to bring out the biological and clinically relevant characteristics of the subtypes. Although some of these schemes capture underlying molecular differences, others predict variations in response to treatment and survival patterns. However, despite this diversity in the approaches, it is clear that molecular mechanisms drive clinical outcomes, and therefore an effective scheme should integrate molecular as well as clinical parameters to enable deeper understanding of cancer mechanisms and allow better decision making in the clinic. Here, using a large cohort of ∼550 breast tumours from The Cancer Genome Atlas, we systematically evaluate a number of expression-based schemes including at least eight molecular pathways implicated in breast cancer and three prognostic signatures, across a variety of classification scenarios covering molecular characteristics, biomarker status, tumour stages and survival patterns. We observe that a careful combination of these schemes yields better classification results compared with using them individually, thus confirming that molecular mechanisms and clinical outcomes are related and that an effective scheme should therefore integrate both these parameters to enable a deeper understanding of the cancer.
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36
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Melchor L, Molyneux G, Mackay A, Magnay FA, Atienza M, Kendrick H, Nava-Rodrigues D, López-García MÁ, Milanezi F, Greenow K, Robertson D, Palacios J, Reis-Filho JS, Smalley MJ. Identification of cellular and genetic drivers of breast cancer heterogeneity in genetically engineered mouse tumour models. J Pathol 2014; 233:124-37. [PMID: 24615332 DOI: 10.1002/path.4345] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 01/24/2014] [Accepted: 02/26/2014] [Indexed: 11/08/2022]
Abstract
The heterogeneous nature of mammary tumours may arise from different initiating genetic lesions occurring in distinct cells of origin. Here, we generated mice in which Brca2, Pten and p53 were depleted in either basal mammary epithelial cells or luminal oestrogen receptor (ER)-negative cells. Basal cell-origin tumours displayed similar histological phenotypes, regardless of the depleted gene. In contrast, luminal ER-negative cells gave rise to diverse phenotypes, depending on the initiating lesions, including both ER-negative and, strikingly, ER-positive invasive ductal carcinomas. Molecular profiling demonstrated that luminal ER-negative cell-origin tumours resembled a range of the molecular subtypes of human breast cancer, including basal-like, luminal B and 'normal-like'. Furthermore, a subset of these tumours resembled the 'claudin-low' tumour subtype. These findings demonstrate that not only do mammary tumour phenotypes depend on the interactions between cell of origin and driver genetic aberrations, but also multiple mammary tumour subtypes, including both ER-positive and -negative disease, can originate from a single epithelial cell type. This is a fundamental advance in our understanding of tumour aetiology.
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MESH Headings
- Animals
- BRCA2 Protein/deficiency
- BRCA2 Protein/genetics
- Breast Neoplasms/genetics
- Breast Neoplasms/metabolism
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/metabolism
- Carcinoma, Ductal, Breast/pathology
- Cell Proliferation
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Claudins/metabolism
- Disease Models, Animal
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Female
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Humans
- Mammary Glands, Animal/metabolism
- Mammary Glands, Animal/pathology
- Mice
- Mice, Knockout
- PTEN Phosphohydrolase/deficiency
- PTEN Phosphohydrolase/genetics
- Phenotype
- Receptors, Estrogen/metabolism
- Time Factors
- Tumor Suppressor Protein p53/deficiency
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Lorenzo Melchor
- Division of Breast Cancer Research, Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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De Summa S, Pinto R, Sambiasi D, Petriella D, Paradiso V, Paradiso A, Tommasi S. BRCAness: a deeper insight into basal-like breast tumors. Ann Oncol 2014; 24 Suppl 8:viii13-viii21. [PMID: 24131964 DOI: 10.1093/annonc/mdt306] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
The molecular scenario of breast cancer has become more complex in the last few years. Distinguishing between BRCA-associated, sporadic, HER2-enriched and triple-negative tumors is not sufficient to allow effective clinical management. Basal-like breast cancer, a subtype of triple-negative breast cancer, differs from others grouped under this heading. Commonalities between BRCA-related tumors and basal-like breast cancers (BRCAness phenotype) are highly relevant to ongoing clinical trials, in particular those investigating targeted therapies (e.g. PARP inhibitors) in sporadic breast tumors. The 'gold standard' to identify basal-like phenotype is DNA microarray, but integrated results could provide a panel of biomarkers helpful in identifying 'BRCAness' tumors (e.g. copy number aberrations, abnormal protein localization and altered transcriptional levels) and other molecular targets, such as APE1,the inhibition of which is emerging as an attractive breast cancer treatment in certain therapeutic settings.
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Affiliation(s)
- S De Summa
- NCRC Istituto Tumori 'Giovanni Paolo II', Bari, Italy
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Leidy J, Khan A, Kandil D. Basal-like breast cancer: update on clinicopathologic, immunohistochemical, and molecular features. Arch Pathol Lab Med 2014; 138:37-43. [PMID: 24377810 DOI: 10.5858/arpa.2012-0439-ra] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
CONTEXT Basal-like breast carcinoma (BLBC) is a distinct molecular subtype of breast carcinoma identified through gene expression profiling studies. OBJECTIVE To provide the clinical background, the histologic profile, and the immunohistochemical profile of these tumors and discuss the current knowledge of their molecular signature and their implications on targeted molecular therapy. DATA SOURCES Data were obtained from review of the pertinent peer-reviewed literature. CONCLUSIONS Basal-like breast carcinomas are aggressive tumors with poor prognosis. Lack of targeted therapy makes their treatment a challenging task. Traditional chemotherapy is still associated with a high risk of relapse and death in a high percentage of patients. Platinum-based chemotherapy has been considered as a candidate for the treatment of BLBCs owing to their BRCA1 phenotype. Approximately 22% of patients treated with single-agent cisplatin show pathologic complete response, which is a comparable rate to that seen with nonplatinum agents. Antiangiogenic agents have been promising, but their currently demonstrated limited response is considered disappointing. Additionally, epidermal growth factor receptor was not shown to be a helpful target for BLBC. A recent study has shown that BLBC appears to be especially sensitive to MEK inhibitors, making it a promising therapeutic possibility. The list of new targets is still evolving and the "magic" therapeutic target is yet to be discovered.
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Affiliation(s)
- Jennifer Leidy
- From the Department of Pathology, University of Massachusetts, UMass Memorial Medical Center, Worcester
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39
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Larsen MJ, Thomassen M, Tan Q, Lænkholm AV, Bak M, Sørensen KP, Andersen MK, Kruse TA, Gerdes AM. RNA profiling reveals familial aggregation of molecular subtypes in non-BRCA1/2 breast cancer families. BMC Med Genomics 2014; 7:9. [PMID: 24479546 PMCID: PMC3909442 DOI: 10.1186/1755-8794-7-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 01/24/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND In more than 70% of families with a strong history of breast and ovarian cancers, pathogenic mutation in BRCA1 or BRCA2 cannot be identified, even though hereditary factors are expected to be involved. It has been proposed that tumors with similar molecular phenotypes also share similar underlying pathophysiological mechanisms. In the current study, the aim was to investigate if global RNA profiling can be used to identify functional subgroups within breast tumors from families tested negative for BRCA1/2 germline mutations and how these subgroupings relate to different breast cancer patients within the same family. METHODS In the current study we analyzed a collection of 70 frozen breast tumor biopsies from a total of 58 families by global RNA profiling and promoter methylation analysis. RESULTS We show that distinct functional subgroupings, similar to the intrinsic molecular breast cancer subtypes, exist among non-BRCA1/2 breast cancers. The distribution of subtypes was markedly different from the distribution found among BRCA1/2 mutation carriers. From 11 breast cancer families, breast tumor biopsies from more than one affected family member were included in the study. Notably, in 8 of these families we found that patients from the same family shared the same tumor subtype, showing a tendency of familial aggregation of tumor subtypes (p-value = 1.7e-3). Using our previously developed BRCA1/2-signatures, we identified 7 non-BRCA1/2 tumors with a BRCA1-like molecular phenotype and provide evidence for epigenetic inactivation of BRCA1 in three of the tumors. In addition, 7 BRCA2-like tumors were found. CONCLUSIONS Our finding indicates involvement of hereditary factors in non-BRCA1/2 breast cancer families in which family members may carry genetic susceptibility not just to breast cancer but to a particular subtype of breast cancer. This is the first study to provide a biological link between breast cancers from family members of high-risk non-BRCA1/2 families in a systematic manner, suggesting that future genetic analysis may benefit from subgrouping families into molecularly homogeneous subtypes in order to search for new high penetrance susceptibility genes.
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Affiliation(s)
- Martin J Larsen
- Department of Clinical Genetics, Odense University Hospital, Sdr, Boulevard 29, Odense 5000, Denmark.
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40
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Srihari S, Raman V, Leong HW, Ragan MA. Evolution and Controllability of Cancer Networks: A Boolean Perspective. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2014; 11:83-94. [PMID: 26355510 DOI: 10.1109/tcbb.2013.128] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cancer forms a robust system capable of maintaining stable functioning (cell sustenance and proliferation) despite perturbations. Cancer progresses as stages over time typically with increasing aggressiveness and worsening prognosis. Characterizing these stages and identifying the genes driving transitions between them is critical to understand cancer progression and to develop effective anti-cancer therapies. In this work, we propose a novel model for the `cancer system' as a Boolean state space in which a Boolean network, built from protein-interaction and gene-expression data from different stages of cancer, transits between Boolean satisfiability states by "editing" interactions and "flipping" genes. Edits reflect rewiring of the PPI network while flipping of genes reflect activation or silencing of genes between stages. We formulate a minimization problem min flip to identify these genes driving the transitions. The application of our model (called BoolSpace) on three case studies-pancreatic and breast tumours in human and post spinal-cord injury (SCI) in rats-reveals valuable insights into the phenomenon of cancer progression: (i) interactions involved in core cell-cycle and DNA-damage repair pathways are significantly rewired in tumours, indicating significant impact to key genome-stabilizing mechanisms; (ii) several of the genes flipped are serine/threonine kinases which act as biological switches, reflecting cellular switching mechanisms between stages; and (iii) different sets of genes are flipped during the initial and final stages indicating a pattern to tumour progression. Based on these results, we hypothesize that robustness of cancer partly stems from "passing of the baton" between genes at different stages-genes from different biological processes and/or cellular components are involved in different stages of tumour progression thereby allowing tumour cells to evade targeted therapy, and therefore an effective therapy should target a "cover set" of these genes. A C/C++ implementation of BoolSpace is freely available at: http://www.bioinformatics.org.au/tools-data.
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41
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Muthuswami M, Ramesh V, Banerjee S, Viveka Thangaraj S, Periasamy J, Bhaskar Rao D, Barnabas GD, Raghavan S, Ganesan K. Breast tumors with elevated expression of 1q candidate genes confer poor clinical outcome and sensitivity to Ras/PI3K inhibition. PLoS One 2013; 8:e77553. [PMID: 24147022 PMCID: PMC3798322 DOI: 10.1371/journal.pone.0077553] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/03/2013] [Indexed: 12/15/2022] Open
Abstract
Genomic aberrations are common in cancers and the long arm of chromosome 1 is known for its frequent amplifications in breast cancer. However, the key candidate genes of 1q, and their contribution in breast cancer pathogenesis remain unexplored. We have analyzed the gene expression profiles of 1635 breast tumor samples using meta-analysis based approach and identified clinically significant candidates from chromosome 1q. Seven candidate genes including exonuclease 1 (EXO1) are consistently over expressed in breast tumors, specifically in high grade and aggressive breast tumors with poor clinical outcome. We derived a EXO1 co-expression module from the mRNA profiles of breast tumors which comprises 1q candidate genes and their co-expressed genes. By integrative functional genomics investigation, we identified the involvement of EGFR, RAS, PI3K / AKT, MYC, E2F signaling in the regulation of these selected 1q genes in breast tumors and breast cancer cell lines. Expression of EXO1 module was found as indicative of elevated cell proliferation, genomic instability, activated RAS/AKT/MYC/E2F1 signaling pathways and loss of p53 activity in breast tumors. mRNA-drug connectivity analysis indicates inhibition of RAS/PI3K as a possible targeted therapeutic approach for the patients with activated EXO1 module in breast tumors. Thus, we identified seven 1q candidate genes strongly associated with the poor survival of breast cancer patients and identified the possibility of targeting them with EGFR/RAS/PI3K inhibitors.
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Affiliation(s)
- Muthulakshmi Muthuswami
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Vignesh Ramesh
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Saikat Banerjee
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Soundara Viveka Thangaraj
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Jayaprakash Periasamy
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Divya Bhaskar Rao
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Georgina D. Barnabas
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
| | - Swetha Raghavan
- Department of Biotechnology, Indian Institute of Technology Madras, Chenna, India
| | - Kumaresan Ganesan
- Cancer Genetics Laboratory, Department of Genetics, Centre for Excellence in Genomic Sciences, School of Biological Sciences, Madurai Kamaraj University, Madurai, India
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Wu X, Li Y, Wang J, Wen X, Marcus MT, Daniels G, Zhang DY, Ye F, Wang LH, Du X, Adams S, Singh B, Zavadil J, Lee P, Monaco ME. Long chain fatty Acyl-CoA synthetase 4 is a biomarker for and mediator of hormone resistance in human breast cancer. PLoS One 2013; 8:e77060. [PMID: 24155918 PMCID: PMC3796543 DOI: 10.1371/journal.pone.0077060] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2013] [Accepted: 09/05/2013] [Indexed: 12/16/2022] Open
Abstract
The purpose of this study was to determine the role of long-chain fatty acyl-CoA synthetase 4 (ACSL4) in breast cancer. Public databases were utilized to analyze the relationship between ACSL4 mRNA expression and the presence of steroid hormone and human epidermal growth factor receptor 2 (HER2) in both breast cancer cell lines and tissue samples. In addition, cell lines were utilized to assess the consequences of either increased or decreased levels of ACSL4 expression. Proliferation, migration, anchorage-independent growth and apoptosis were used as biological end points. Effects on mRNA expression and signal transduction pathways were also monitored. A meta-analysis of public gene expression databases indicated that ACSL4 expression is positively correlated with a unique subtype of triple negative breast cancer (TNBC), characterized by the absence of androgen receptor (AR) and therefore referred to as quadruple negative breast cancer (QNBC). Results of experiments in breast cancer cell lines suggest that simultaneous expression of ACSL4 and a receptor is associated with hormone resistance. Forced expression of ACSL4 in ACSL4-negative, estrogen receptor α (ER)-positive MCF-7 cells resulted in increased growth, invasion and anchorage independent growth, as well as a loss of dependence on estrogen that was accompanied by a reduction in the levels of steroid hormone receptors. Sensitivity to tamoxifen, triacsin C and etoposide was also attenuated. Similarly, when HER2-positive, ACSL4-negative, SKBr3 breast cancer cells were induced to express ACSL4, the proliferation rate increased and the apoptotic effect of lapatinib was reduced. The growth stimulatory effect of ACSL4 expression was also observed in vivo in nude mice when MCF-7 control and ACSL4-expressing cells were utilized to induce tumors. Our data strongly suggest that ACSL4 can serve as both a biomarker for, and mediator of, an aggressive breast cancer phenotype.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Apoptosis/drug effects
- Apoptosis/genetics
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Breast Neoplasms/classification
- Breast Neoplasms/drug therapy
- Breast Neoplasms/enzymology
- Breast Neoplasms/genetics
- Cell Adhesion
- Cell Line, Tumor
- Cell Proliferation
- Coenzyme A Ligases/genetics
- Coenzyme A Ligases/metabolism
- Drug Resistance, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Estrogen Receptor alpha/genetics
- Estrogen Receptor alpha/metabolism
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic/drug effects
- Hormones/pharmacology
- Humans
- Mice
- Mice, Nude
- Neoplasm Invasiveness
- Oligonucleotide Array Sequence Analysis
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Receptor, ErbB-2/genetics
- Receptor, ErbB-2/metabolism
- Reproducibility of Results
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Affiliation(s)
- Xinyu Wu
- Department of Neuroscience & Physiology, New York University School of Medicine, New York, New York, United States of America
| | - Yirong Li
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Jinhua Wang
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
- NYU Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, United States of America
| | - Xin Wen
- Department of Pediatrics, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
- NYU Center for Health Informatics and Bioinformatics, New York University School of Medicine, New York, New York, United States of America
| | - Max T. Marcus
- Department of Neuroscience & Physiology, New York University School of Medicine, New York, New York, United States of America
| | - Garrett Daniels
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - David Y. Zhang
- Department of Pathology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Fei Ye
- Department of Pathology, Mount Sinai School of Medicine, New York, New York, United States of America
| | - Ling Hang Wang
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Xinxin Du
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
| | - Sylvia Adams
- Department of Medicine, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
| | - Baljit Singh
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
| | - Jiri Zavadil
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
| | - Peng Lee
- Department of Pathology, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
- VA New York Harbor Healthcare System, New York, New York, United States of America
- *E-mail: (MM); (PL)
| | - Marie E. Monaco
- Department of Neuroscience & Physiology, New York University School of Medicine, New York, New York, United States of America
- NYU Cancer Institute, New York University School of Medicine, New York, New York, United States of America
- VA New York Harbor Healthcare System, New York, New York, United States of America
- *E-mail: (MM); (PL)
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Day TK, Bianco-Miotto T. Common gene pathways and families altered by DNA methylation in breast and prostate cancers. Endocr Relat Cancer 2013; 20:R215-32. [PMID: 23818572 DOI: 10.1530/erc-13-0204] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Epigenetic modifications, such as DNA methylation, are widely studied in cancer as they are stable and easy to measure genome wide. DNA methylation changes have been used to differentiate benign from malignant tissue and to predict tumor recurrence or patient outcome. Multiple genome wide DNA methylation studies in breast and prostate cancers have identified genes that are differentially methylated in malignant tissue compared with non-malignant tissue or in association with hormone receptor status or tumor recurrence. Although this has identified potential biomarkers for diagnosis and prognosis, what is highlighted by reviewing these studies is the similarities between breast and prostate cancers. In particular, the gene families/pathways targeted by DNA methylation in breast and prostate cancers have significant overlap and include homeobox genes, zinc finger transcription factors, S100 calcium binding proteins, and potassium voltage-gated family members. Many of the gene pathways targeted by aberrant methylation in breast and prostate cancers are not targeted in other cancers, suggesting that some of these targets may be specific to hormonal cancers. Genome wide DNA methylation profiles in breast and prostate cancers will not only define more specific and sensitive biomarkers for cancer diagnosis and prognosis but also identify novel therapeutic targets, which may be direct targets of agents that reverse DNA methylation or which may target novel gene families that are themselves DNA methylation targets.
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Affiliation(s)
- Tanya K Day
- Dame Roma Mitchell Cancer Research Laboratories, Discipline of Medicine, Hanson Institute, Adelaide Prostate Cancer Research Centre, The University of Adelaide, South Australia, Australia
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Chen GK, Chang X, Curtis C, Wang K. Precise inference of copy number alterations in tumor samples from SNP arrays. ACTA ACUST UNITED AC 2013; 29:2964-70. [PMID: 24021380 DOI: 10.1093/bioinformatics/btt521] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
MOTIVATION The accurate detection of copy number alterations (CNAs) in human genomes is important for understanding susceptibility to cancer and mechanisms of tumor progression. CNA detection in tumors from single nucleotide polymorphism (SNP) genotyping arrays is a challenging problem due to phenomena such as aneuploidy, stromal contamination, genomic waves and intra-tumor heterogeneity, issues that leading methods do not optimally address. RESULTS Here we introduce methods and software (PennCNV-tumor) for fast and accurate CNA detection using signal intensity data from SNP genotyping arrays. We estimate stromal contamination by applying a maximum likelihood approach over multiple discrete genomic intervals. By conditioning on signal intensity across the genome, our method accounts for both aneuploidy and genomic waves. Finally, our method uses a hidden Markov model to integrate multiple sources of information, including total and allele-specific signal intensity at each SNP, as well as physical maps to make posterior inferences of CNAs. Using real data from cancer cell-lines and patient tumors, we demonstrate substantial improvements in accuracy and computational efficiency compared with existing methods.
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Affiliation(s)
- Gary K Chen
- Department of Preventive Medicine, Zilkha Neurogenetic Institute and Department of Psychiatry, University of Southern California, Los Angeles, CA 90089, USA
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Mohan P, Castellsague J, Jiang J, Allen K, Chen H, Nemirovsky O, Spyra M, Hu K, Kluwe L, Pujana MA, Villanueva A, Mautner VF, Keats JJ, Dunn SE, Lazaro C, Maxwell CA. Genomic imbalance of HMMR/RHAMM regulates the sensitivity and response of malignant peripheral nerve sheath tumour cells to aurora kinase inhibition. Oncotarget 2013; 4:80-93. [PMID: 23328114 PMCID: PMC3702209 DOI: 10.18632/oncotarget.793] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Malignant peripheral nerve sheath tumours (MPNST) are rare, hereditary cancers associated with neurofibromatosis type I. MPNSTs lack effective treatment options as they often resist chemotherapies and have high rates of disease recurrence. Aurora kinase A (AURKA) is an emerging target in cancer and an aurora kinase inhibitor (AKI), termed MLN8237, shows promise against MPNST cell lines in vitro and in vivo. Here, we test MLN8237 against two primary human MPNST grown in vivo as xenotransplants and find that treatment results in tumour cells exiting the cell cycle and undergoing endoreduplication, which cumulates in stabilized disease. Targeted therapies can often fail in the clinic due to insufficient knowledge about factors that determine tumour susceptibilities, so we turned to three MPNST cell-lines to further study and modulate the cellular responses to AKI. We find that the sensitivity of cell-lines with amplification of AURKA depends upon the activity of the kinase, which correlates with the expression of the regulatory gene products TPX2 and HMMR/RHAMM. Silencing of HMMR/RHAMM, but not TPX2, augments AURKA activity and sensitizes MPNST cells to AKI. Furthermore, we find that AURKA activity is critical to the propagation and self-renewal of sphere-enriched MPNST cancer stem-like cells. AKI treatment significantly reduces the formation of spheroids, attenuates the self-renewal of spheroid forming cells, and promotes their differentiation. Moreover, silencing of HMMR/RHAMM is sufficient to endow MPNST cells with an ability to form and maintain sphere culture. Collectively, our data indicate that AURKA is a rationale therapeutic target for MPNST and tumour cell responses to AKI, which include differentiation, are modulated by the abundance of HMMR/RHAMM.
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Affiliation(s)
- Pooja Mohan
- Department of Pediatrics, Child and Family Research Institute, University of British Columbia, Vancouver, British Columbia, Canada
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Gorrini C, Baniasadi PS, Harris IS, Silvester J, Inoue S, Snow B, Joshi PA, Wakeham A, Molyneux SD, Martin B, Bouwman P, Cescon DW, Elia AJ, Winterton-Perks Z, Cruickshank J, Brenner D, Tseng A, Musgrave M, Berman HK, Khokha R, Jonkers J, Mak TW, Gauthier ML. BRCA1 interacts with Nrf2 to regulate antioxidant signaling and cell survival. ACTA ACUST UNITED AC 2013; 210:1529-44. [PMID: 23857982 PMCID: PMC3727320 DOI: 10.1084/jem.20121337] [Citation(s) in RCA: 207] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
BRCA1 deficiency results in impaired Nrf2-mediated antioxidant responses followed by cell death, with estradiol rescuing the effect by inducing Nrf2 stabilization. Oxidative stress plays an important role in cancer development and treatment. Recent data implicate the tumor suppressor BRCA1 in regulating oxidative stress, but the molecular mechanism and the impact in BRCA1-associated tumorigenesis remain unclear. Here, we show that BRCA1 regulates Nrf2-dependent antioxidant signaling by physically interacting with Nrf2 and promoting its stability and activation. BRCA1-deficient mouse primary mammary epithelial cells show low expression of Nrf2-regulated antioxidant enzymes and accumulate reactive oxygen species (ROS) that impair survival in vivo. Increased Nrf2 activation rescues survival and ROS levels in BRCA1-null cells. Interestingly, 53BP1 inactivation, which has been shown to alleviate several defects associated with BRCA1 loss, rescues survival of BRCA1-null cells without restoring ROS levels. We demonstrate that estrogen treatment partially restores Nrf2 levels in the absence of BRCA1. Our data suggest that Nrf2-regulated antioxidant response plays a crucial role in controlling survival downstream of BRCA1 loss. The ability of estrogen to induce Nrf2 posits an involvement of an estrogen-Nrf2 connection in BRCA1 tumor suppression. Lastly, BRCA1-mutated tumors retain a defective antioxidant response that increases the sensitivity to oxidative stress. In conclusion, the role of BRCA1 in regulating Nrf2 activity suggests important implications for both the etiology and treatment of BRCA1-related cancers.
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Affiliation(s)
- Chiara Gorrini
- The Campbell Family Institute for Breast Cancer Research, University Health Network, Toronto, Ontario M5G 2M9, Canada
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Pécuchet N, Popova T, Manié E, Lucchesi C, Battistella A, Vincent-Salomon A, Caux-Moncoutier V, Bollet M, Sigal-Zafrani B, Sastre-Garau X, Stoppa-Lyonnet D, Stern MH. Loss of heterozygosity at 13q13 and 14q32 predicts BRCA2 inactivation in luminal breast carcinomas. Int J Cancer 2013; 133:2834-42. [PMID: 23754601 DOI: 10.1002/ijc.28315] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2013] [Revised: 04/26/2013] [Accepted: 05/14/2013] [Indexed: 11/11/2022]
Abstract
BRCA2 is the major high-penetrance predisposition gene for luminal (estrogen receptor [ER] positive) breast cancers. However, many BRCA2 mutant carriers lack family history of breast/ovarian cancers and do not benefit from genetic testing. Specific genomic features associated with BRCA2 inactivation in tumors could help identify patients for whom a genetic test for BRCA2 may be proposed. A series of ER-positive invasive ductal carcinomas (IDCs) including 30 carriers of BRCA2 mutations and 215 control cases was studied by single-nucleotide polymorphism (SNP) arrays. Cases and controls were stratified by grade and HER2 status. Independently, 7 BRCA2 and 51 control cases were used for validation. Absolute copy number and Loss of heterozygosity (LOH) profiles were obtained from SNP arrays by the genome alteration print (GAP) method. BRCA2 tumors were observed to display a discriminatively greater number of chromosomal breaks calculated after filtering out and smoothing <3 Mb variations. This argues for a BRCA2-associated genomic instability responsible for long-segment aberrations. Co-occurrence of two genomic features-LOH of 13q13 and 14q32-was found to predict BRCA2 status with 90% of sensitivity and 87% of specificity in discovery series of high-grade HER2-negative IDCs and 100% of sensitivity and 88% of specificity in an independent series of 58 IDCs. Estimated positive predictive value was 17.2% (confidence interval: 6.7-33.5) in the whole series. In conclusion, the simplified BRCA2 classifier based on the co-occurrence of LOH at 13q13 and 14q32 could provide an indication to test for BRCA2 mutation in patients with ER-positive IDC.
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Affiliation(s)
- Nicolas Pécuchet
- Institut Curie, Centre de Recherche, Paris, France; INSERM U830, Paris, France; Department of Tumor Biology, Institut Curie, Paris, France
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Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. J Transl Med 2013; 93:701-10. [PMID: 23568031 DOI: 10.1038/labinvest.2013.54] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Pathology archives contain vast resources of clinical material in the form of formalin-fixed paraffin-embedded (FFPE) tissue samples. Owing to the methods of tissue fixation and storage, the integrity of DNA and RNA available from FFPE tissue is compromized, which means obtaining informative data regarding epigenetic, genomic, and expression alterations can be challenging. Here, we have investigated the utility of repairing damaged DNA derived from FFPE tumors prior to single-nucleotide polymorphism (SNP) arrays for whole-genome DNA copy number analysis. DNA was extracted from FFPE samples spanning five decades, involving tumor material obtained from surgical specimens and postmortems. Various aspects of the protocol were assessed, including the method of DNA extraction, the role of Quality Control quantitative PCR (qPCR) in predicting sample success, and the effect of DNA restoration on assay performance, data quality, and the prediction of copy number aberrations (CNAs). DNA that had undergone the repair process yielded higher SNP call rates, reduced log R ratio variance, and improved calling of CNAs compared with matched FFPE DNA not subjected to repair. Reproducible mapping of genomic break points and detection of focal CNAs representing high-level gains and homozygous deletions (HD) were possible, even on autopsy material obtained in 1974. For example, DNA amplifications at the ERBB2 and EGFR gene loci and a HD mapping to 13q14.2 were validated using immunohistochemistry, in situ hybridization, and qPCR. The power of SNP arrays lies in the detection of allele-specific aberrations; however, this aspect of the analysis remains challenging, particularly in the distinction between loss of heterozygosity (LOH) and copy neutral LOH. In summary, attempting to repair DNA that is damaged during fixation and storage may be a useful pretreatment step for genomic studies of large archival FFPE cohorts with long-term follow-up or for understanding rare cancer types, where fresh frozen material is scarce.
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Larsen MJ, Kruse TA, Tan Q, Lænkholm AV, Bak M, Lykkesfeldt AE, Sørensen KP, Hansen TVO, Ejlertsen B, Gerdes AM, Thomassen M. Classifications within molecular subtypes enables identification of BRCA1/BRCA2 mutation carriers by RNA tumor profiling. PLoS One 2013; 8:e64268. [PMID: 23704984 PMCID: PMC3660328 DOI: 10.1371/journal.pone.0064268] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2012] [Accepted: 04/11/2013] [Indexed: 12/30/2022] Open
Abstract
Pathogenic germline mutations in BRCA1 or BRCA2 are detected in less than one third of families with a strong history of breast cancer. It is therefore expected that mutations still remain undetected by currently used screening methods. In addition, a growing number of BRCA1/2 sequence variants of unclear pathogen significance are found in the families, constituting an increasing clinical challenge. New methods are therefore needed to improve the detection rate and aid the interpretation of the clinically uncertain variants. In this study we analyzed a series of 33 BRCA1, 22 BRCA2, and 128 sporadic tumors by RNA profiling to investigate the classification potential of RNA profiles to predict BRCA1/2 mutation status. We found that breast tumors from BRCA1 and BRCA2 mutation carriers display characteristic RNA expression patterns, allowing them to be distinguished from sporadic tumors. The majority of BRCA1 tumors were basal-like while BRCA2 tumors were mainly luminal B. Using RNA profiles, we were able to distinguish BRCA1 tumors from sporadic tumors among basal-like tumors with 83% accuracy and BRCA2 from sporadic tumors among luminal B tumors with 89% accuracy. Furthermore, subtype-specific BRCA1/2 gene signatures were successfully validated in two independent data sets with high accuracies. Although additional validation studies are required, indication of BRCA1/2 involvement (“BRCAness”) by RNA profiling could potentially be valuable as a tool for distinguishing pathogenic mutations from benign variants, for identification of undetected mutation carriers, and for selecting patients sensitive to new therapeutics such as PARP inhibitors.
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Affiliation(s)
- Martin J. Larsen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
- * E-mail:
| | - Torben A. Kruse
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Qihua Tan
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Epidemiology, Institute of Public Health, University of Southern Denmark, Odense, Denmark
| | | | - Martin Bak
- Department of Pathology, Odense University Hospital, Odense, Denmark
| | - Anne E. Lykkesfeldt
- Breast Cancer Group, Unit of Cell Death and Metabolism, Danish Cancer Society Research Center, Copenhagen, Denmark
| | - Kristina P. Sørensen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
| | - Thomas v. O. Hansen
- Center for Genomic Medicine, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Bent Ejlertsen
- Danish Breast Cancer Cooperative Group Statistical Center, Department of Oncology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mads Thomassen
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Human Genetics, Clinical Institute, University of Southern Denmark, Odense, Denmark
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Srihari S, Ragan MA. Systematic tracking of dysregulated modules identifies novel genes in cancer. Bioinformatics 2013; 29:1553-61. [DOI: 10.1093/bioinformatics/btt191] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
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